Starting phenix.real_space_refine
on Tue Jun 10 09:16:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsh_32758/06_2025/7wsh_32758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsh_32758/06_2025/7wsh_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_32758/06_2025/7wsh_32758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsh_32758/06_2025/7wsh_32758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsh_32758/06_2025/7wsh_32758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsh_32758/06_2025/7wsh_32758.cif"
  }
  resolution = 2.89
  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=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.09, per 1000 atoms: 0.79
  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: 1.59
  Conformation dependent library (CDL) restraints added in 962.4 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: 0.65
  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: 1.69

  Time building geometry restraints manager: 1.90 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: 3704
       15.23 -    30.46: 177
       30.46 -    45.68: 48
       45.68 -    60.91: 9
       60.91 -    76.14: 2
  Dihedral angle restraints: 3940
    sinusoidal: 1611
      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 3937 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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.960
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:12.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
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  : 10.058  76.137   2425
  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 (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: -0.03 (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
 TRP   0.008   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.009   0.001   PHE A 428 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00021 (    1)
  link_NAG-ASN         : angle       1.52209 (    3)
  hydrogen bonds       : bond        0.25386 (  318)
  hydrogen bonds       : angle       8.24951 (  912)
  metal coordination   : bond        0.00038 (    2)
  SS BOND              : bond        0.00359 (    7)
  SS BOND              : angle       0.79094 (   14)
  covalent geometry    : bond        0.00256 ( 6641)
  covalent geometry    : angle       0.44519 ( 9025)

*********************** 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  : 0.773 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7481 (tp40) cc_final: 0.7241 (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: 1.2540
  time to fit residues: 204.7077
Evaluate side-chains
  102 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 45 optimal weight:    0.2980
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3719 r_free = 0.3719 target = 0.153135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.120762 restraints weight = 7184.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.78
r_work: 0.3175 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6651  Z= 0.137
  Angle     :  0.525   6.045   9042  Z= 0.278
  Chirality :  0.042   0.149    938
  Planarity :  0.004   0.035   1172
  Dihedral  :  5.047  50.391    892
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.06 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.34 (0.29), residues: 789
  helix:  0.41 (0.26), residues: 398
  sheet:  0.51 (0.78), residues: 43
  loop :  0.17 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.010   0.001   PHE A 428 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.008   0.001   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       1.46416 (    3)
  hydrogen bonds       : bond        0.05278 (  318)
  hydrogen bonds       : angle       5.52983 (  912)
  metal coordination   : bond        0.00067 (    2)
  SS BOND              : bond        0.00604 (    7)
  SS BOND              : angle       1.02747 (   14)
  covalent geometry    : bond        0.00289 ( 6641)
  covalent geometry    : angle       0.52346 ( 9025)

*********************** 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
  120 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7757 (tp40) cc_final: 0.7290 (tp40)
REVERT: A  114 GLN cc_start: 0.7839 (pt0) cc_final: 0.7379 (tp-100)
REVERT: A  171 GLU cc_start: 0.7891 (mp0) cc_final: 0.7659 (mm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 1.1916
  time to fit residues: 141.6047
Evaluate side-chains
  100 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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 68 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 325 GLN
A 401 HIS
A 522 GLN
B 354 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.151226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117937 restraints weight = 7320.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.82
r_work: 0.3160 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6651  Z= 0.142
  Angle     :  0.500   5.576   9042  Z= 0.261
  Chirality :  0.042   0.135    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.858  39.295    892
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.34 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.29), residues: 789
  helix:  0.54 (0.26), residues: 403
  sheet:  0.56 (0.81), residues: 43
  loop :  0.16 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.025   0.001   PHE A 314 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.005   0.001   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00077 (    1)
  link_NAG-ASN         : angle       1.60025 (    3)
  hydrogen bonds       : bond        0.04911 (  318)
  hydrogen bonds       : angle       5.22120 (  912)
  metal coordination   : bond        0.00155 (    2)
  SS BOND              : bond        0.00499 (    7)
  SS BOND              : angle       1.02051 (   14)
  covalent geometry    : bond        0.00315 ( 6641)
  covalent geometry    : angle       0.49777 ( 9025)

*********************** 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: 20
    poor density    : 102
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.7758 (tp40) cc_final: 0.7357 (tp40)
REVERT: A  114 GLN cc_start: 0.7801 (pt0) cc_final: 0.7316 (tp-100)
REVERT: A  470 LYS cc_start: 0.8532 (mttp) cc_final: 0.8234 (mtmm)
REVERT: A  578 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7821 (p0)
  outliers start: 20
  outliers final: 10
  residues processed: 114
  average time/residue: 1.2696
  time to fit residues: 151.7127
Evaluate side-chains
  102 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 73 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 322 ASN
A 325 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.150623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.117198 restraints weight = 7407.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.84
r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2196

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= 0.135
  Angle     :  0.500   5.693   9042  Z= 0.260
  Chirality :  0.041   0.140    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.653  31.058    891
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.35 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.55 (0.29), residues: 789
  helix:  0.62 (0.26), residues: 403
  sheet:  0.40 (0.79), residues: 43
  loop :  0.24 (0.33), residues: 343

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00062 (    1)
  link_NAG-ASN         : angle       1.68322 (    3)
  hydrogen bonds       : bond        0.04616 (  318)
  hydrogen bonds       : angle       5.14607 (  912)
  metal coordination   : bond        0.00086 (    2)
  SS BOND              : bond        0.00441 (    7)
  SS BOND              : angle       0.98443 (   14)
  covalent geometry    : bond        0.00298 ( 6641)
  covalent geometry    : angle       0.49796 ( 9025)

*********************** 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
  111 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: A   79 GLN cc_start: 0.7741 (tp40) cc_final: 0.7135 (tp-100)
REVERT: A   98 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7382 (tt0)
REVERT: A  114 GLN cc_start: 0.7842 (pt0) cc_final: 0.7340 (tp-100)
REVERT: A  171 GLU cc_start: 0.7877 (mp0) cc_final: 0.7447 (mp0)
REVERT: A  470 LYS cc_start: 0.8549 (mttp) cc_final: 0.8249 (mtmm)
REVERT: A  578 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7901 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 1.2706
  time to fit residues: 138.9651
Evaluate side-chains
  101 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 61 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 322 ASN
A 325 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 = 0.152407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119345 restraints weight = 7326.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.81
r_work: 0.3159 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6651  Z= 0.113
  Angle     :  0.482   5.479   9042  Z= 0.250
  Chirality :  0.040   0.128    938
  Planarity :  0.004   0.036   1172
  Dihedral  :  4.458  26.488    891
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 15.35 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.65 (0.29), residues: 789
  helix:  0.72 (0.26), residues: 403
  sheet:  0.30 (0.77), residues: 43
  loop :  0.29 (0.33), residues: 343

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00081 (    1)
  link_NAG-ASN         : angle       1.72916 (    3)
  hydrogen bonds       : bond        0.04359 (  318)
  hydrogen bonds       : angle       5.02507 (  912)
  metal coordination   : bond        0.00048 (    2)
  SS BOND              : bond        0.00410 (    7)
  SS BOND              : angle       0.93216 (   14)
  covalent geometry    : bond        0.00240 ( 6641)
  covalent geometry    : angle       0.47971 ( 9025)

*********************** 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
  116 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A   79 GLN cc_start: 0.7718 (tp40) cc_final: 0.7161 (tp-100)
REVERT: A  114 GLN cc_start: 0.7826 (pt0) cc_final: 0.7319 (tp-100)
REVERT: A  171 GLU cc_start: 0.7886 (mp0) cc_final: 0.7674 (mp0)
REVERT: A  470 LYS cc_start: 0.8523 (mttp) cc_final: 0.8225 (mtmm)
REVERT: A  578 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7909 (p0)
  outliers start: 19
  outliers final: 9
  residues processed: 107
  average time/residue: 1.2597
  time to fit residues: 141.5439
Evaluate side-chains
  104 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
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  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  443 SER
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 16 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   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  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 = 0.3680 r_free = 0.3680 target = 0.149992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.116643 restraints weight = 7305.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.82
r_work: 0.3152 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2382

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= 0.133
  Angle     :  0.491   6.049   9042  Z= 0.255
  Chirality :  0.041   0.151    938
  Planarity :  0.004   0.040   1172
  Dihedral  :  4.427  26.939    891
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.21 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.68 (0.29), residues: 789
  helix:  0.73 (0.26), residues: 404
  sheet:  0.36 (0.77), residues: 43
  loop :  0.31 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.017   0.001   PHE A 314 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.007   0.001   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00025 (    1)
  link_NAG-ASN         : angle       1.80414 (    3)
  hydrogen bonds       : bond        0.04477 (  318)
  hydrogen bonds       : angle       5.00670 (  912)
  metal coordination   : bond        0.00095 (    2)
  SS BOND              : bond        0.00450 (    7)
  SS BOND              : angle       0.99004 (   14)
  covalent geometry    : bond        0.00294 ( 6641)
  covalent geometry    : angle       0.48930 ( 9025)

*********************** 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: 21
    poor density    : 99
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: A   79 GLN cc_start: 0.7727 (tp40) cc_final: 0.7174 (tp-100)
REVERT: A  114 GLN cc_start: 0.7827 (pt0) cc_final: 0.7333 (tp-100)
REVERT: A  470 LYS cc_start: 0.8546 (mttp) cc_final: 0.8255 (mtmm)
REVERT: A  578 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7930 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 112
  average time/residue: 1.2493
  time to fit residues: 147.0271
Evaluate side-chains
  106 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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 34 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 322 ASN
A 325 GLN
B 493 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.150471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.117224 restraints weight = 7289.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.82
r_work: 0.3133 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6651  Z= 0.157
  Angle     :  0.515   6.177   9042  Z= 0.267
  Chirality :  0.042   0.147    938
  Planarity :  0.004   0.057   1172
  Dihedral  :  4.525  26.984    891
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.93 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.64 (0.29), residues: 789
  helix:  0.72 (0.26), residues: 404
  sheet:  0.35 (0.78), residues: 43
  loop :  0.28 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A 314 
 TYR   0.022   0.001   TYR A 385 
 ARG   0.007   0.001   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.79999 (    3)
  hydrogen bonds       : bond        0.04624 (  318)
  hydrogen bonds       : angle       5.05483 (  912)
  metal coordination   : bond        0.00101 (    2)
  SS BOND              : bond        0.00531 (    7)
  SS BOND              : angle       1.06310 (   14)
  covalent geometry    : bond        0.00356 ( 6641)
  covalent geometry    : angle       0.51260 ( 9025)

*********************** 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
  119 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7471 (tm-30)
REVERT: A   79 GLN cc_start: 0.7729 (tp40) cc_final: 0.7170 (tp-100)
REVERT: A   98 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7389 (tt0)
REVERT: A  114 GLN cc_start: 0.7842 (pt0) cc_final: 0.7175 (tp-100)
REVERT: A  470 LYS cc_start: 0.8518 (mttp) cc_final: 0.8218 (mtmm)
REVERT: A  578 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7889 (p0)
  outliers start: 23
  outliers final: 13
  residues processed: 111
  average time/residue: 1.1176
  time to fit residues: 130.7523
Evaluate side-chains
  107 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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   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  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 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   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  98 GLN
A 322 ASN
A 325 GLN
A 401 HIS
B 493 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.152287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119339 restraints weight = 7360.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 1.79
r_work: 0.3169 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2527

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= 0.132
  Angle     :  0.505   6.284   9042  Z= 0.261
  Chirality :  0.041   0.141    938
  Planarity :  0.004   0.048   1172
  Dihedral  :  4.477  26.533    891
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.64 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.78 (0.29), residues: 789
  helix:  0.85 (0.26), residues: 396
  sheet:  0.39 (0.78), residues: 43
  loop :  0.32 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A 314 
 TYR   0.026   0.001   TYR B 505 
 ARG   0.010   0.001   ARG A 600 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00042 (    1)
  link_NAG-ASN         : angle       1.77292 (    3)
  hydrogen bonds       : bond        0.04449 (  318)
  hydrogen bonds       : angle       5.01375 (  912)
  metal coordination   : bond        0.00078 (    2)
  SS BOND              : bond        0.00436 (    7)
  SS BOND              : angle       0.98678 (   14)
  covalent geometry    : bond        0.00290 ( 6641)
  covalent geometry    : angle       0.50276 ( 9025)

*********************** 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
  115 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7426 (tm-30)
REVERT: A   79 GLN cc_start: 0.7780 (tp40) cc_final: 0.7260 (tp-100)
REVERT: A  114 GLN cc_start: 0.7812 (pt0) cc_final: 0.7186 (tp-100)
REVERT: A  470 LYS cc_start: 0.8533 (mttp) cc_final: 0.8254 (mtmm)
REVERT: A  578 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7897 (p0)
  outliers start: 20
  outliers final: 11
  residues processed: 108
  average time/residue: 1.2093
  time to fit residues: 137.3477
Evaluate side-chains
  105 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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  111 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  440 ASN
Chi-restraints excluded: chain B residue  443 SER
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 75 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0060
   chunk 69 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    0.3980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
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 = 0.3731 r_free = 0.3731 target = 0.154187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121204 restraints weight = 7369.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.77
r_work: 0.3177 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6651  Z= 0.112
  Angle     :  0.489   6.393   9042  Z= 0.252
  Chirality :  0.040   0.136    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.349  25.864    891
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.64 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.93 (0.29), residues: 789
  helix:  1.05 (0.26), residues: 390
  sheet:  0.42 (0.78), residues: 43
  loop :  0.30 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A 314 
 TYR   0.020   0.001   TYR A 183 
 ARG   0.005   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       1.72854 (    3)
  hydrogen bonds       : bond        0.04184 (  318)
  hydrogen bonds       : angle       4.95609 (  912)
  metal coordination   : bond        0.00101 (    2)
  SS BOND              : bond        0.00351 (    7)
  SS BOND              : angle       0.89761 (   14)
  covalent geometry    : bond        0.00239 ( 6641)
  covalent geometry    : angle       0.48674 ( 9025)

*********************** 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
  110 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7476 (tm-30)
REVERT: A   79 GLN cc_start: 0.7727 (tp40) cc_final: 0.7201 (tp-100)
REVERT: A  114 GLN cc_start: 0.7773 (pt0) cc_final: 0.7128 (tp-100)
REVERT: A  406 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8450 (mm-30)
REVERT: A  470 LYS cc_start: 0.8468 (mttp) cc_final: 0.8174 (mtmm)
REVERT: A  578 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7866 (p0)
REVERT: A  600 ARG cc_start: 0.7557 (ptm160) cc_final: 0.7297 (mtt-85)
REVERT: B  414 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7852 (tp40)
REVERT: B  494 SER cc_start: 0.8637 (m) cc_final: 0.8324 (t)
  outliers start: 16
  outliers final: 10
  residues processed: 106
  average time/residue: 1.5477
  time to fit residues: 172.1090
Evaluate side-chains
  100 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 63 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    0.2980
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
A 325 GLN
A 599 ASN
B 493 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.155250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.121991 restraints weight = 7362.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.83
r_work: 0.3178 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6651  Z= 0.109
  Angle     :  0.496   6.439   9042  Z= 0.254
  Chirality :  0.040   0.142    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.219  19.389    890
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.93 %
    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 (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:  1.01 (0.29), residues: 789
  helix:  1.13 (0.26), residues: 390
  sheet:  0.40 (0.78), residues: 43
  loop :  0.34 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.016   0.001   PHE A 314 
 TYR   0.015   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00099 (    1)
  link_NAG-ASN         : angle       1.70014 (    3)
  hydrogen bonds       : bond        0.04120 (  318)
  hydrogen bonds       : angle       4.93406 (  912)
  metal coordination   : bond        0.00373 (    2)
  SS BOND              : bond        0.00324 (    7)
  SS BOND              : angle       0.87938 (   14)
  covalent geometry    : bond        0.00230 ( 6641)
  covalent geometry    : angle       0.49444 ( 9025)

********************** 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
  111 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7410 (tm-30)
REVERT: A   79 GLN cc_start: 0.7763 (tp40) cc_final: 0.7269 (tp-100)
REVERT: A  114 GLN cc_start: 0.7787 (pt0) cc_final: 0.7136 (tp-100)
REVERT: A  189 GLU cc_start: 0.7893 (tt0) cc_final: 0.7526 (tp30)
REVERT: A  406 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: A  470 LYS cc_start: 0.8499 (mttp) cc_final: 0.8227 (mtmm)
REVERT: A  578 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7897 (p0)
REVERT: A  600 ARG cc_start: 0.7570 (ptm160) cc_final: 0.7370 (mmt90)
REVERT: B  414 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7923 (tp40)
REVERT: B  494 SER cc_start: 0.8600 (m) cc_final: 0.8302 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 104
  average time/residue: 1.3421
  time to fit residues: 147.5541
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  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  111 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0980
   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 322 ASN
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.154406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.121005 restraints weight = 7469.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.84
r_work: 0.3172 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6651  Z= 0.125
  Angle     :  0.517   7.643   9042  Z= 0.264
  Chirality :  0.041   0.142    938
  Planarity :  0.004   0.037   1172
  Dihedral  :  4.274  19.358    890
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.22 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.00 (0.29), residues: 789
  helix:  1.12 (0.26), residues: 391
  sheet:  0.40 (0.78), residues: 43
  loop :  0.34 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.001   PHE B 347 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A 156 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       1.71663 (    3)
  hydrogen bonds       : bond        0.04249 (  318)
  hydrogen bonds       : angle       4.97276 (  912)
  metal coordination   : bond        0.00135 (    2)
  SS BOND              : bond        0.00385 (    7)
  SS BOND              : angle       0.93706 (   14)
  covalent geometry    : bond        0.00276 ( 6641)
  covalent geometry    : angle       0.51485 ( 9025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6822.77 seconds
wall clock time: 121 minutes 36.67 seconds (7296.67 seconds total)