Starting phenix.real_space_refine
on Fri Jul  3 02:00:07 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wsh_32758/07_2026/7wsh_32758.cif"
  }
  resolution = 2.89
  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=   0.061
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 6216 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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4119      2.51       5
     N    1082      2.21       5
     O    1218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6457
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4899
          Classifications: {'peptide': 598}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 568}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.10, per 1000 atoms: 0.17
  Number of scatterers: 6457
  At special positions: 0
  Unit cell: (72.921, 84.963, 127.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1218      8.00
     N    1082      7.00
     C    4119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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 B 601 " - " ASN B 343 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 327.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "


  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      56.9% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.720A  pdb=" N   GLU A  38 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.655A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.550A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 194
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 4.074A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN A 232 " --> pdb=" O   GLN A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.835A  pdb=" N   ASP A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    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 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.562A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.589A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.610A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 414
      removed outlier: 3.688A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   THR A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
      removed outlier: 3.577A  pdb=" N   ASN A 437 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.636A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 4.083A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.835A  pdb=" N   MET A 557 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.827A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.556A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.971A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 3.522A  pdb=" N   THR A 347 " --> pdb=" O   LYS A 359 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.559A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    318 hydrogen bonds defined for protein.
    912 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: 0.86

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2086
        1.34 -     1.46: 1704
        1.46 -     1.58: 2793
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6641
  Sorted by residual:
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.63e+00
  bond pdb=" C5  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" C3  NAG B 601 "
       pdb=" O3  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.02e+00
  bond pdb=" CA  ILE A  54 "
       pdb=" CB  ILE A  54 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 7.03e-01
  bond pdb=" C2  NAG B 601 "
       pdb=" N2  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.453 -0.014 2.00e-02 2.50e+03 5.22e-01
  ... (remaining 6636 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.02: 8743
        1.02 -     2.03: 212
        2.03 -     3.05: 46
        3.05 -     4.07: 16
        4.07 -     5.09: 8
  Bond angle restraints: 9025
  Sorted by residual:
  angle pdb=" CA  GLY A 352 "
        pdb=" C   GLY A 352 "
        pdb=" N   LYS A 353 "
      ideal   model   delta    sigma   weight residual
     114.23  117.49   -3.26 8.80e-01 1.29e+00 1.37e+01
  angle pdb=" CA  GLY A 352 "
        pdb=" C   GLY A 352 "
        pdb=" O   GLY A 352 "
      ideal   model   delta    sigma   weight residual
     122.33  119.83    2.50 8.10e-01 1.52e+00 9.53e+00
  angle pdb=" CA  GLN A 101 "
        pdb=" C   GLN A 101 "
        pdb=" N   HIS A 102 "
      ideal   model   delta    sigma   weight residual
     118.27  121.46   -3.19 1.59e+00 3.96e-01 4.02e+00
  angle pdb=" N   GLY A 352 "
        pdb=" CA  GLY A 352 "
        pdb=" C   GLY A 352 "
      ideal   model   delta    sigma   weight residual
     111.85  109.84    2.01 1.06e+00 8.90e-01 3.61e+00
  angle pdb=" N   GLY B 496 "
        pdb=" CA  GLY B 496 "
        pdb=" C   GLY B 496 "
      ideal   model   delta    sigma   weight residual
     113.18  109.00    4.18 2.37e+00 1.78e-01 3.11e+00
  ... (remaining 9020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.23: 3687
       15.23 -    30.46: 177
       30.46 -    45.68: 46
       45.68 -    60.91: 7
       60.91 -    76.14: 2
  Dihedral angle restraints: 3919
    sinusoidal: 1590
      harmonic: 2329
  Sorted by residual:
  dihedral pdb=" CA  VAL A 342 "
           pdb=" C   VAL A 342 "
           pdb=" N   VAL A 343 "
           pdb=" CA  VAL A 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.48   15.52     0      5.00e+00 4.00e-02 9.64e+00
  dihedral pdb=" N   GLN B 493 "
           pdb=" CA  GLN B 493 "
           pdb=" CB  GLN B 493 "
           pdb=" CG  GLN B 493 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.71  -54.29     3      1.50e+01 4.44e-03 9.27e+00
  dihedral pdb=" CA  TYR A 497 "
           pdb=" C   TYR A 497 "
           pdb=" N   CYS A 498 "
           pdb=" CA  CYS A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.82   15.18     0      5.00e+00 4.00e-02 9.21e+00
  ... (remaining 3916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 487
       0.025 -    0.050: 279
       0.050 -    0.075: 108
       0.075 -    0.100: 45
       0.100 -    0.124: 19
  Chirality restraints: 938
  Sorted by residual:
  chirality pdb=" CA  ILE A  88 "
            pdb=" N   ILE A  88 "
            pdb=" C   ILE A  88 "
            pdb=" CB  ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality pdb=" CA  VAL A 343 "
            pdb=" N   VAL A 343 "
            pdb=" C   VAL A 343 "
            pdb=" CB  VAL A 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.38e-01
  ... (remaining 935 not shown)

  Planarity restraints: 1173
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 520 "    0.019 5.00e-02 4.00e+02   2.95e-02 1.39e+00
        pdb=" N   PRO B 521 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 521 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 521 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "   -0.019 5.00e-02 4.00e+02   2.88e-02 1.32e+00
        pdb=" N   PRO A 583 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 388 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 389 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 389 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 389 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1170 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 123
        2.69 -     3.24: 6431
        3.24 -     3.80: 10582
        3.80 -     4.35: 15128
        4.35 -     4.90: 24081
  Nonbonded interactions: 56345
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.152 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     2.163 2.230
  nonbonded pdb=" O   ASN B 439 "
            pdb=" OG  SER B 443 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OG1 THR A 276 "
            pdb=" OG1 THR A 445 "
     model   vdw
     2.282 3.040
  ... (remaining 56340 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:             4.770
  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:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.660
  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:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6651  Z= 0.115
  Angle     :  0.447   5.085   9042  Z= 0.237
  Chirality :  0.039   0.124    938
  Planarity :  0.003   0.030   1172
  Dihedral  :  9.901  76.137   2404
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  3.87 %
    Favored  : 95.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.03 (0.29), residues: 789
  helix:  0.03 (0.26), residues: 391
  sheet:  0.80 (0.87), residues: 41
  loop :  0.02 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 454 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.009   0.001   PHE A 428 
 TRP   0.008   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.12 ( 6641)
  covalent geometry    : angle       0.44519 /  0.24 ( 9025)
  SS BOND              : bond        0.00359 /  0.18 (    7)
  SS BOND              : angle       0.79094 /  0.50 (   14)
  hydrogen bonds       : bond        0.25386 / 16.98 (  318)
  hydrogen bonds       : angle       8.24951 /  5.96 (  912)
  metal coordination   : bond        0.00038 /  0.02 (    2)
  link_NAG-ASN         : bond        0.00021 /  0.01 (    1)
  link_NAG-ASN         : angle       1.52209 /  0.89 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 153
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7481 (tp40) cc_final: 0.7242 (tp40)
REVERT: A  114 GLN cc_start: 0.7554 (pt0) cc_final: 0.7232 (tp-100)
REVERT: A  332 MET cc_start: 0.7917 (ttp) cc_final: 0.7660 (ttp)
  outliers start: 5
  outliers final: 2
  residues processed: 156
  average time/residue: 0.5059
  time to fit residues: 82.6597
Evaluate side-chains
  101 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   82 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    0.0060
   overall best weight:    0.5596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 228 GLN
A 325 GLN
A 522 GLN
A 586 ASN
B 354 ASN
B 409 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121060 restraints weight = 7340.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.80
r_work: 0.3187 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6651  Z= 0.132
  Angle     :  0.520   6.145   9042  Z= 0.275
  Chirality :  0.041   0.144    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.238  26.799    871
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.63 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.28 (0.29), residues: 789
  helix:  0.35 (0.25), residues: 406
  sheet:  0.60 (0.79), residues: 43
  loop :  0.13 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 600 
 TYR   0.021   0.001   TYR A 385 
 PHE   0.009   0.001   PHE A 428 
 TRP   0.013   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 ( 6641)
  covalent geometry    : angle       0.51821 /  0.27 ( 9025)
  SS BOND              : bond        0.00472 /  0.24 (    7)
  SS BOND              : angle       1.00979 /  0.64 (   14)
  hydrogen bonds       : bond        0.05406 /  3.79 (  318)
  hydrogen bonds       : angle       5.52067 /  3.99 (  912)
  metal coordination   : bond        0.00105 /  0.05 (    2)
  link_NAG-ASN         : bond        0.00186 /  0.10 (    1)
  link_NAG-ASN         : angle       1.38030 /  0.81 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7759 (tp40) cc_final: 0.7300 (tp40)
REVERT: A  114 GLN cc_start: 0.7848 (pt0) cc_final: 0.7363 (tp-100)
REVERT: A  171 GLU cc_start: 0.7867 (mp0) cc_final: 0.7650 (mm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 114
  average time/residue: 0.5568
  time to fit residues: 66.7343
Evaluate side-chains
  97 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 THR
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 24 optimal weight:    6.9990
   chunk 17 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 325 GLN
A 401 HIS
B 354 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.151146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.117628 restraints weight = 7374.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.83
r_work: 0.3180 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6651  Z= 0.124
  Angle     :  0.487   5.604   9042  Z= 0.255
  Chirality :  0.041   0.132    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.246  27.170    871
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.34 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.47 (0.29), residues: 789
  helix:  0.56 (0.26), residues: 403
  sheet:  0.50 (0.79), residues: 43
  loop :  0.18 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 340 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.023   0.001   PHE A 314 
 TRP   0.013   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 6641)
  covalent geometry    : angle       0.48527 /  0.25 ( 9025)
  SS BOND              : bond        0.00545 /  0.28 (    7)
  SS BOND              : angle       0.95256 /  0.59 (   14)
  hydrogen bonds       : bond        0.04769 /  3.39 (  318)
  hydrogen bonds       : angle       5.19630 /  3.76 (  912)
  metal coordination   : bond        0.00096 /  0.05 (    2)
  link_NAG-ASN         : bond        0.00123 /  0.06 (    1)
  link_NAG-ASN         : angle       1.35002 /  0.79 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7754 (tp40) cc_final: 0.7360 (tp40)
REVERT: A  114 GLN cc_start: 0.7807 (pt0) cc_final: 0.7313 (tp-100)
REVERT: A  171 GLU cc_start: 0.7937 (mp0) cc_final: 0.7717 (mp0)
REVERT: A  470 LYS cc_start: 0.8519 (mttp) cc_final: 0.8217 (mtmm)
REVERT: A  578 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7762 (p0)
  outliers start: 21
  outliers final: 7
  residues processed: 113
  average time/residue: 0.5867
  time to fit residues: 69.7836
Evaluate side-chains
  98 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  472 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 325 GLN
A 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.152167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.118819 restraints weight = 7414.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 1.83
r_work: 0.3145 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6651  Z= 0.136
  Angle     :  0.500   5.792   9042  Z= 0.260
  Chirality :  0.041   0.143    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.283  26.963    870
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.35 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.58 (0.29), residues: 789
  helix:  0.62 (0.26), residues: 404
  sheet:  0.38 (0.78), residues: 43
  loop :  0.29 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 403 
 TYR   0.021   0.001   TYR A 385 
 PHE   0.020   0.001   PHE A 314 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.14 ( 6641)
  covalent geometry    : angle       0.49806 /  0.26 ( 9025)
  SS BOND              : bond        0.00474 /  0.24 (    7)
  SS BOND              : angle       0.99936 /  0.63 (   14)
  hydrogen bonds       : bond        0.04632 /  3.29 (  318)
  hydrogen bonds       : angle       5.09668 /  3.69 (  912)
  metal coordination   : bond        0.00168 /  0.08 (    2)
  link_NAG-ASN         : bond        0.00058 /  0.03 (    1)
  link_NAG-ASN         : angle       1.41477 /  0.82 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7726 (tp40) cc_final: 0.7222 (tp40)
REVERT: A  114 GLN cc_start: 0.7798 (pt0) cc_final: 0.7323 (tp-100)
REVERT: A  171 GLU cc_start: 0.7941 (mp0) cc_final: 0.7710 (OUTLIER)
REVERT: A  470 LYS cc_start: 0.8567 (mttp) cc_final: 0.8273 (mtmm)
REVERT: A  578 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7850 (p0)
  outliers start: 23
  outliers final: 15
  residues processed: 114
  average time/residue: 0.5643
  time to fit residues: 67.7492
Evaluate side-chains
  105 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   87 GLU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 325 GLN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.150669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.116967 restraints weight = 7484.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.85
r_work: 0.3155 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6651  Z= 0.128
  Angle     :  0.489   5.582   9042  Z= 0.254
  Chirality :  0.041   0.132    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.261  26.738    870
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.35 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.64 (0.29), residues: 789
  helix:  0.68 (0.26), residues: 404
  sheet:  0.27 (0.76), residues: 43
  loop :  0.33 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 600 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.018   0.001   PHE A 314 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 6641)
  covalent geometry    : angle       0.48722 /  0.25 ( 9025)
  SS BOND              : bond        0.00437 /  0.22 (    7)
  SS BOND              : angle       0.97071 /  0.63 (   14)
  hydrogen bonds       : bond        0.04470 /  3.18 (  318)
  hydrogen bonds       : angle       5.01191 /  3.62 (  912)
  metal coordination   : bond        0.00066 /  0.03 (    2)
  link_NAG-ASN         : bond        0.00060 /  0.03 (    1)
  link_NAG-ASN         : angle       1.41138 /  0.82 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A   79 GLN cc_start: 0.7737 (tp40) cc_final: 0.7188 (tp-100)
REVERT: A   98 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7382 (tt0)
REVERT: A  114 GLN cc_start: 0.7811 (pt0) cc_final: 0.7338 (tp-100)
REVERT: A  470 LYS cc_start: 0.8535 (mttp) cc_final: 0.8246 (mtmm)
REVERT: A  578 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7915 (p0)
  outliers start: 21
  outliers final: 11
  residues processed: 108
  average time/residue: 0.5949
  time to fit residues: 67.5334
Evaluate side-chains
  107 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0570
   chunk 27 optimal weight:    0.0770
   chunk 24 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.5456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 ASN
A 325 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.151202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.117895 restraints weight = 7466.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.82
r_work: 0.3175 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6651  Z= 0.115
  Angle     :  0.479   5.942   9042  Z= 0.250
  Chirality :  0.040   0.143    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.218  26.558    870
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.49 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.29), residues: 789
  helix:  0.78 (0.26), residues: 402
  sheet:  0.32 (0.76), residues: 43
  loop :  0.37 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 600 
 TYR   0.019   0.001   TYR A 385 
 PHE   0.017   0.001   PHE A 314 
 TRP   0.017   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6641)
  covalent geometry    : angle       0.47739 /  0.25 ( 9025)
  SS BOND              : bond        0.00385 /  0.19 (    7)
  SS BOND              : angle       0.91505 /  0.59 (   14)
  hydrogen bonds       : bond        0.04351 /  3.09 (  318)
  hydrogen bonds       : angle       4.99918 /  3.61 (  912)
  metal coordination   : bond        0.00051 /  0.02 (    2)
  link_NAG-ASN         : bond        0.00092 /  0.05 (    1)
  link_NAG-ASN         : angle       1.39570 /  0.81 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7473 (tm-30)
REVERT: A   79 GLN cc_start: 0.7778 (tp40) cc_final: 0.7263 (tp-100)
REVERT: A  114 GLN cc_start: 0.7777 (pt0) cc_final: 0.7338 (tp-100)
REVERT: A  171 GLU cc_start: 0.7968 (mp0) cc_final: 0.7447 (mp0)
REVERT: A  175 GLN cc_start: 0.8803 (mt0) cc_final: 0.8549 (mt0)
REVERT: A  470 LYS cc_start: 0.8532 (mttp) cc_final: 0.8260 (mtmm)
REVERT: A  578 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7903 (p0)
REVERT: B  494 SER cc_start: 0.8585 (m) cc_final: 0.8315 (t)
  outliers start: 22
  outliers final: 13
  residues processed: 112
  average time/residue: 0.5957
  time to fit residues: 70.1197
Evaluate side-chains
  104 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 299 ASN
A 322 ASN
A 325 GLN
A 401 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.153184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.119930 restraints weight = 7337.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 1.82
r_work: 0.3169 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6651  Z= 0.129
  Angle     :  0.493   6.257   9042  Z= 0.256
  Chirality :  0.041   0.142    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.265  26.572    870
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.36 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.29), residues: 789
  helix:  0.78 (0.26), residues: 404
  sheet:  0.39 (0.77), residues: 43
  loop :  0.36 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 600 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.016   0.001   PHE A 314 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 ( 6641)
  covalent geometry    : angle       0.49159 /  0.26 ( 9025)
  SS BOND              : bond        0.00407 /  0.21 (    7)
  SS BOND              : angle       0.96265 /  0.63 (   14)
  hydrogen bonds       : bond        0.04407 /  3.13 (  318)
  hydrogen bonds       : angle       5.00309 /  3.62 (  912)
  metal coordination   : bond        0.00074 /  0.04 (    2)
  link_NAG-ASN         : bond        0.00040 /  0.02 (    1)
  link_NAG-ASN         : angle       1.43710 /  0.84 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7735 (tp40) cc_final: 0.7195 (tp-100)
REVERT: A  114 GLN cc_start: 0.7793 (pt0) cc_final: 0.7327 (tp-100)
REVERT: A  171 GLU cc_start: 0.7943 (mp0) cc_final: 0.7575 (mp0)
REVERT: A  175 GLN cc_start: 0.8802 (mt0) cc_final: 0.8598 (mt0)
REVERT: A  189 GLU cc_start: 0.7953 (tt0) cc_final: 0.7574 (tp30)
REVERT: A  470 LYS cc_start: 0.8514 (mttp) cc_final: 0.8234 (mtmm)
REVERT: A  578 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7907 (p0)
REVERT: A  600 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7187 (ptm160)
REVERT: B  494 SER cc_start: 0.8634 (m) cc_final: 0.8334 (t)
  outliers start: 24
  outliers final: 12
  residues processed: 108
  average time/residue: 0.5138
  time to fit residues: 58.5563
Evaluate side-chains
  102 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0470
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0170
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 322 ASN
A 325 GLN
A 556 GLN
A 599 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.155444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.122132 restraints weight = 7352.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 1.82
r_work: 0.3198 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6651  Z= 0.105
  Angle     :  0.474   6.246   9042  Z= 0.247
  Chirality :  0.040   0.138    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.154  25.362    870
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.64 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.90 (0.29), residues: 789
  helix:  0.98 (0.26), residues: 399
  sheet:  0.49 (0.77), residues: 43
  loop :  0.33 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.017   0.001   PHE A 314 
 TRP   0.017   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.10 ( 6641)
  covalent geometry    : angle       0.47237 /  0.25 ( 9025)
  SS BOND              : bond        0.00382 /  0.20 (    7)
  SS BOND              : angle       0.85206 /  0.55 (   14)
  hydrogen bonds       : bond        0.04108 /  2.92 (  318)
  hydrogen bonds       : angle       4.93534 /  3.57 (  912)
  metal coordination   : bond        0.00033 /  0.02 (    2)
  link_NAG-ASN         : bond        0.00124 /  0.07 (    1)
  link_NAG-ASN         : angle       1.33645 /  0.78 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7757 (tp40) cc_final: 0.7264 (tp-100)
REVERT: A   98 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7301 (tt0)
REVERT: A  114 GLN cc_start: 0.7780 (pt0) cc_final: 0.7133 (tp-100)
REVERT: A  171 GLU cc_start: 0.7902 (mp0) cc_final: 0.7576 (mp0)
REVERT: A  600 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7237 (ptm160)
REVERT: B  494 SER cc_start: 0.8574 (m) cc_final: 0.8305 (t)
  outliers start: 21
  outliers final: 11
  residues processed: 113
  average time/residue: 0.5046
  time to fit residues: 60.2828
Evaluate side-chains
  103 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   98 GLN
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  98 GLN
A 175 GLN
A 325 GLN
A 401 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.154115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121027 restraints weight = 7451.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.82
r_work: 0.3211 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6651  Z= 0.115
  Angle     :  0.495   7.467   9042  Z= 0.257
  Chirality :  0.041   0.136    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.063  17.104    869
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.79 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.29), residues: 789
  helix:  1.04 (0.26), residues: 397
  sheet:  0.49 (0.77), residues: 43
  loop :  0.35 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.021   0.001   TYR A 183 
 PHE   0.016   0.001   PHE A 314 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 6641)
  covalent geometry    : angle       0.49375 /  0.26 ( 9025)
  SS BOND              : bond        0.00352 /  0.18 (    7)
  SS BOND              : angle       0.87194 /  0.61 (   14)
  hydrogen bonds       : bond        0.04196 /  2.98 (  318)
  hydrogen bonds       : angle       4.97593 /  3.60 (  912)
  metal coordination   : bond        0.00131 /  0.07 (    2)
  link_NAG-ASN         : bond        0.00105 /  0.06 (    1)
  link_NAG-ASN         : angle       1.35343 /  0.79 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7763 (tp40) cc_final: 0.7282 (tp-100)
REVERT: A  114 GLN cc_start: 0.7758 (pt0) cc_final: 0.7149 (tp-100)
REVERT: A  600 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7261 (ptm160)
REVERT: B  494 SER cc_start: 0.8584 (m) cc_final: 0.8310 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 0.5544
  time to fit residues: 60.8393
Evaluate side-chains
  104 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.153932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.121033 restraints weight = 7249.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 1.80
r_work: 0.3216 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6651  Z= 0.124
  Angle     :  0.519   7.941   9042  Z= 0.270
  Chirality :  0.041   0.138    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.107  16.928    869
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 18.51 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.93 (0.29), residues: 789
  helix:  0.99 (0.26), residues: 398
  sheet:  0.47 (0.77), residues: 43
  loop :  0.37 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.015   0.001   PHE A 314 
 TRP   0.016   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6641)
  covalent geometry    : angle       0.51791 /  0.27 ( 9025)
  SS BOND              : bond        0.00377 /  0.19 (    7)
  SS BOND              : angle       0.89663 /  0.64 (   14)
  hydrogen bonds       : bond        0.04260 /  3.03 (  318)
  hydrogen bonds       : angle       5.00207 /  3.62 (  912)
  metal coordination   : bond        0.00124 /  0.06 (    2)
  link_NAG-ASN         : bond        0.00075 /  0.04 (    1)
  link_NAG-ASN         : angle       1.37818 /  0.80 (    3)

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7762 (tp40) cc_final: 0.7282 (tp-100)
REVERT: A   98 GLN cc_start: 0.7695 (tt0) cc_final: 0.7435 (tt0)
REVERT: A  114 GLN cc_start: 0.7753 (pt0) cc_final: 0.7154 (tp-100)
REVERT: A  600 ARG cc_start: 0.7667 (mmm-85) cc_final: 0.7295 (ptm160)
REVERT: B  494 SER cc_start: 0.8583 (m) cc_final: 0.8292 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 104
  average time/residue: 0.5415
  time to fit residues: 59.5775
Evaluate side-chains
  103 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 ASP
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.0030
   chunk 8 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0970
   chunk 39 optimal weight:    0.8980
   chunk 74 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.3788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.122774 restraints weight = 7345.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.81
r_work: 0.3240 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6651  Z= 0.107
  Angle     :  0.512   8.697   9042  Z= 0.266
  Chirality :  0.041   0.144    938
  Planarity :  0.004   0.035   1172
  Dihedral  :  4.048  16.443    869
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.79 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.97 (0.29), residues: 789
  helix:  1.07 (0.26), residues: 398
  sheet:  0.46 (0.76), residues: 43
  loop :  0.33 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 600 
 TYR   0.019   0.001   TYR A 183 
 PHE   0.016   0.001   PHE A 314 
 TRP   0.018   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.11 ( 6641)
  covalent geometry    : angle       0.51077 /  0.27 ( 9025)
  SS BOND              : bond        0.00289 /  0.15 (    7)
  SS BOND              : angle       0.83549 /  0.58 (   14)
  hydrogen bonds       : bond        0.04077 /  2.88 (  318)
  hydrogen bonds       : angle       4.96309 /  3.59 (  912)
  metal coordination   : bond        0.00041 /  0.02 (    2)
  link_NAG-ASN         : bond        0.00125 /  0.07 (    1)
  link_NAG-ASN         : angle       1.33497 /  0.78 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2717.68 seconds
wall clock time: 47 minutes 2.12 seconds (2822.12 seconds total)