Starting phenix.real_space_refine
on Sat May 10 15:51:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wrh_37776/05_2025/8wrh_37776.cif"
  }
  resolution = 3.08
  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=   0.001 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4137      2.51       5
     N    1069      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6459
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 27, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 1558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1558
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.38, per 1000 atoms: 0.83
  Number of scatterers: 6459
  At special positions: 0
  Unit cell: (71.912, 89.688, 117.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1216      8.00
     N    1069      7.00
     C    4137      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, 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=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " 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=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 546 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 322 "
      " NAG A 904 " - " ASN A  53 "
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 972.5 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      54.9% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.620A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 154
      removed outlier: 3.568A  pdb=" N   ASN A 154 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.517A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.871A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
      removed outlier: 3.794A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.837A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.504A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.672A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.547A  pdb=" N   GLU A 483 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.141A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.570A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.774A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.723A  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 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.655A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.554A  pdb=" N   PHE B 371 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.669A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 390'
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 417 through 422
      removed outlier: 3.537A  pdb=" N   TYR B 421 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.571A  pdb=" N   GLN B 506 " --> pdb=" O   VAL B 503 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.527A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358
      removed outlier: 3.757A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.406A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454
      removed outlier: 8.338A  pdb=" N   ASN B 450 " --> pdb=" O   SER B 494 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   SER B 494 " --> pdb=" O   ASN B 450 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   LEU B 452 " --> pdb=" O   LEU B 492 " (cutoff:3.500A)
      removed outlier: 8.623A  pdb=" N   LEU B 492 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)

    302 hydrogen bonds defined for protein.
    858 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: 1.81

  Time building geometry restraints manager: 1.97 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1257
        1.33 -     1.45: 1774
        1.45 -     1.57: 3555
        1.57 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6644
  Sorted by residual:
  bond pdb=" N   TYR B 489 "
       pdb=" CA  TYR B 489 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.04e+01
  bond pdb=" CA  ALA A  80 "
       pdb=" CB  ALA A  80 "
    ideal  model  delta    sigma   weight residual
    1.534  1.483  0.050 1.58e-02 4.01e+03 1.02e+01
  bond pdb=" N   ASN B 487 "
       pdb=" CA  ASN B 487 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.034 1.19e-02 7.06e+03 8.06e+00
  bond pdb=" CA  TYR B 489 "
       pdb=" C   TYR B 489 "
    ideal  model  delta    sigma   weight residual
    1.523  1.487  0.036 1.34e-02 5.57e+03 7.11e+00
  bond pdb=" N   PRO B 486 "
       pdb=" CA  PRO B 486 "
    ideal  model  delta    sigma   weight residual
    1.473  1.440  0.033 1.32e-02 5.74e+03 6.22e+00
  ... (remaining 6639 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 8929
        2.62 -     5.24: 87
        5.24 -     7.86: 13
        7.86 -    10.48: 1
       10.48 -    13.10: 1
  Bond angle restraints: 9031
  Sorted by residual:
  angle pdb=" N   TYR B 489 "
        pdb=" CA  TYR B 489 "
        pdb=" CB  TYR B 489 "
      ideal   model   delta    sigma   weight residual
     110.49  123.59  -13.10 1.69e+00 3.50e-01 6.01e+01
  angle pdb=" CA  PHE B 455 "
        pdb=" CB  PHE B 455 "
        pdb=" CG  PHE B 455 "
      ideal   model   delta    sigma   weight residual
     113.80  121.46   -7.66 1.00e+00 1.00e+00 5.87e+01
  angle pdb=" N   ALA A  80 "
        pdb=" CA  ALA A  80 "
        pdb=" C   ALA A  80 "
      ideal   model   delta    sigma   weight residual
     113.50  105.68    7.82 1.23e+00 6.61e-01 4.04e+01
  angle pdb=" N   LEU A  79 "
        pdb=" CA  LEU A  79 "
        pdb=" C   LEU A  79 "
      ideal   model   delta    sigma   weight residual
     113.30  106.59    6.71 1.34e+00 5.57e-01 2.50e+01
  angle pdb=" N   VAL B 483 "
        pdb=" CA  VAL B 483 "
        pdb=" C   VAL B 483 "
      ideal   model   delta    sigma   weight residual
     109.34  119.45  -10.11 2.08e+00 2.31e-01 2.36e+01
  ... (remaining 9026 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.80: 3457
       20.80 -    41.59: 394
       41.59 -    62.39: 103
       62.39 -    83.18: 13
       83.18 -   103.98: 11
  Dihedral angle restraints: 3978
    sinusoidal: 1658
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.28  -48.28     1      1.00e+01 1.00e-02 3.21e+01
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.98   48.02     1      1.00e+01 1.00e-02 3.18e+01
  dihedral pdb=" CA  CYS B 361 "
           pdb=" C   CYS B 361 "
           pdb=" N   VAL B 362 "
           pdb=" CA  VAL B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.39   26.61     0      5.00e+00 4.00e-02 2.83e+01
  ... (remaining 3975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 749
       0.050 -    0.099: 164
       0.099 -    0.149: 36
       0.149 -    0.198: 2
       0.198 -    0.248: 3
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CA  CYS B 488 "
            pdb=" N   CYS B 488 "
            pdb=" C   CYS B 488 "
            pdb=" CB  CYS B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  TYR B 489 "
            pdb=" N   TYR B 489 "
            pdb=" C   TYR B 489 "
            pdb=" CB  TYR B 489 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  LEU A  79 "
            pdb=" N   LEU A  79 "
            pdb=" C   LEU A  79 "
            pdb=" CB  LEU A  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 951 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 482 "    0.023 2.00e-02 2.50e+03   4.54e-02 2.07e+01
        pdb=" C   GLY B 482 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   GLY B 482 "    0.030 2.00e-02 2.50e+03
        pdb=" N   VAL B 483 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 483 "    0.013 2.00e-02 2.50e+03   2.62e-02 6.87e+00
        pdb=" C   VAL B 483 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   VAL B 483 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA B 484 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 455 "    0.019 2.00e-02 2.50e+03   1.73e-02 5.25e+00
        pdb=" CG  PHE B 455 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 455 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 455 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 455 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 455 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 455 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 172
        2.70 -     3.25: 6326
        3.25 -     3.80: 10667
        3.80 -     4.35: 13447
        4.35 -     4.90: 22970
  Nonbonded interactions: 53582
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   ASP A 499 "
            pdb=" OG  SER A 502 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OE1 GLN A 102 "
            pdb=" OH  TYR A 202 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" OD2 ASP B 467 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OG  SER B 438 "
            pdb=" OD2 ASP B 442 "
     model   vdw
     2.216 3.040
  ... (remaining 53577 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:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.830
  Find NCS groups from input model:        0.100
  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:3.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6654  Z= 0.209
  Angle     :  0.678  13.100   9055  Z= 0.375
  Chirality :  0.045   0.248    954
  Planarity :  0.004   0.045   1166
  Dihedral  : 18.702 103.977   2470
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  4.83 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 24.64 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.30), residues: 786
  helix:  1.21 (0.26), residues: 396
  sheet:  0.89 (0.81), residues: 44
  loop : -1.13 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.040   0.002   PHE B 455 
 TYR   0.021   0.002   TYR A 279 
 ARG   0.003   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00112 (    4)
  link_NAG-ASN         : angle       1.43160 (   12)
  hydrogen bonds       : bond        0.12653 (  302)
  hydrogen bonds       : angle       5.87823 (  858)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       0.91632 (   12)
  covalent geometry    : bond        0.00403 ( 6644)
  covalent geometry    : angle       0.67571 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.8023 (mtp) cc_final: 0.7782 (mtp)
REVERT: A  478 TRP cc_start: 0.6722 (m100) cc_final: 0.6478 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1551
  time to fit residues: 18.6961
Evaluate side-chains
  83 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0670
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0970
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.3716

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.188962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.146582 restraints weight = 7262.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.27
r_work: 0.3471 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6654  Z= 0.114
  Angle     :  0.535   7.236   9055  Z= 0.266
  Chirality :  0.042   0.188    954
  Planarity :  0.004   0.043   1166
  Dihedral  :  7.340  60.270    940
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.33 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 23.49 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.30), residues: 786
  helix:  1.49 (0.26), residues: 396
  sheet:  0.99 (0.78), residues: 44
  loop : -1.22 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.003   0.000   HIS A  34 
 PHE   0.016   0.001   PHE B 455 
 TYR   0.009   0.001   TYR A  41 
 ARG   0.003   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    4)
  link_NAG-ASN         : angle       1.64886 (   12)
  hydrogen bonds       : bond        0.03985 (  302)
  hydrogen bonds       : angle       4.68060 (  858)
  SS BOND              : bond        0.00357 (    6)
  SS BOND              : angle       0.96264 (   12)
  covalent geometry    : bond        0.00253 ( 6644)
  covalent geometry    : angle       0.53102 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.7987 (mtp) cc_final: 0.7567 (mtp)
REVERT: A  347 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (p)
REVERT: A  360 MET cc_start: 0.6732 (ptm) cc_final: 0.6423 (ptm)
REVERT: A  364 VAL cc_start: 0.7765 (t) cc_final: 0.7452 (t)
REVERT: A  544 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7114 (mt)
REVERT: B  500 THR cc_start: 0.8597 (p) cc_final: 0.8357 (p)
  outliers start: 10
  outliers final: 4
  residues processed: 95
  average time/residue: 0.1631
  time to fit residues: 21.6241
Evaluate side-chains
  87 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  338 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 102 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.181711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.139898 restraints weight = 7393.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.31
r_work: 0.3390 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   6654  Z= 0.193
  Angle     :  0.592   7.460   9055  Z= 0.296
  Chirality :  0.044   0.171    954
  Planarity :  0.004   0.041   1166
  Dihedral  :  5.271  31.790    940
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.05 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.30), residues: 786
  helix:  1.38 (0.26), residues: 394
  sheet:  0.78 (0.76), residues: 42
  loop : -1.16 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.002   PHE B 455 
 TYR   0.019   0.002   TYR A 385 
 ARG   0.005   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00158 (    4)
  link_NAG-ASN         : angle       2.33487 (   12)
  hydrogen bonds       : bond        0.04723 (  302)
  hydrogen bonds       : angle       4.68944 (  858)
  SS BOND              : bond        0.00451 (    6)
  SS BOND              : angle       1.36523 (   12)
  covalent geometry    : bond        0.00466 ( 6644)
  covalent geometry    : angle       0.58452 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 TYR cc_start: 0.7645 (m-80) cc_final: 0.7030 (m-80)
REVERT: A  347 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8588 (p)
REVERT: A  360 MET cc_start: 0.7315 (ptm) cc_final: 0.7032 (ptm)
REVERT: A  364 VAL cc_start: 0.7855 (t) cc_final: 0.7550 (t)
REVERT: A  467 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3817 (pm20)
REVERT: A  544 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7048 (mt)
  outliers start: 19
  outliers final: 12
  residues processed: 103
  average time/residue: 0.1639
  time to fit residues: 23.4110
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  467 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0270
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.9040

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.182614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141996 restraints weight = 7404.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.15
r_work: 0.3422 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6654  Z= 0.144
  Angle     :  0.543   7.403   9055  Z= 0.271
  Chirality :  0.042   0.145    954
  Planarity :  0.004   0.042   1166
  Dihedral  :  4.840  28.298    940
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.90 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.30), residues: 786
  helix:  1.41 (0.26), residues: 396
  sheet:  0.04 (0.76), residues: 49
  loop : -1.24 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.014   0.001   PHE B 455 
 TYR   0.018   0.001   TYR A 279 
 ARG   0.006   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00067 (    4)
  link_NAG-ASN         : angle       2.14103 (   12)
  hydrogen bonds       : bond        0.04181 (  302)
  hydrogen bonds       : angle       4.56484 (  858)
  SS BOND              : bond        0.00405 (    6)
  SS BOND              : angle       0.99346 (   12)
  covalent geometry    : bond        0.00342 ( 6644)
  covalent geometry    : angle       0.53727 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8220 (m-80)
REVERT: A  225 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6542 (m-30)
REVERT: A  259 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6399 (pt)
REVERT: A  347 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8605 (p)
REVERT: A  360 MET cc_start: 0.7245 (ptm) cc_final: 0.6950 (ptm)
REVERT: A  364 VAL cc_start: 0.7953 (t) cc_final: 0.7665 (t)
REVERT: A  544 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7139 (mt)
REVERT: B  500 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8270 (p)
  outliers start: 20
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1477
  time to fit residues: 21.4163
Evaluate side-chains
  98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141422 restraints weight = 7274.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.12
r_work: 0.3423 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6654  Z= 0.136
  Angle     :  0.526   7.376   9055  Z= 0.262
  Chirality :  0.041   0.142    954
  Planarity :  0.004   0.043   1166
  Dihedral  :  4.524  25.359    940
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.19 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.30), residues: 786
  helix:  1.50 (0.27), residues: 396
  sheet:  0.66 (0.77), residues: 42
  loop : -1.22 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 566 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.012   0.001   PHE B 455 
 TYR   0.020   0.001   TYR A 279 
 ARG   0.005   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00097 (    4)
  link_NAG-ASN         : angle       2.06636 (   12)
  hydrogen bonds       : bond        0.04101 (  302)
  hydrogen bonds       : angle       4.49106 (  858)
  SS BOND              : bond        0.00370 (    6)
  SS BOND              : angle       1.03227 (   12)
  covalent geometry    : bond        0.00323 ( 6644)
  covalent geometry    : angle       0.52014 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8213 (m-80)
REVERT: A  225 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6493 (m-30)
REVERT: A  347 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8580 (p)
REVERT: A  360 MET cc_start: 0.7228 (ptm) cc_final: 0.6929 (ptm)
REVERT: A  364 VAL cc_start: 0.8019 (t) cc_final: 0.7727 (t)
REVERT: A  467 GLU cc_start: 0.4383 (OUTLIER) cc_final: 0.3189 (pt0)
REVERT: A  544 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7145 (mt)
REVERT: B  466 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.4792 (ttm170)
REVERT: B  500 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (p)
  outliers start: 20
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1651
  time to fit residues: 24.1873
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 508 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.181373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.141600 restraints weight = 7284.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.08
r_work: 0.3455 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6654  Z= 0.127
  Angle     :  0.518   7.325   9055  Z= 0.258
  Chirality :  0.041   0.139    954
  Planarity :  0.004   0.043   1166
  Dihedral  :  4.352  24.599    940
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 22.77 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.30), residues: 786
  helix:  1.69 (0.27), residues: 391
  sheet:  0.65 (0.77), residues: 44
  loop : -1.25 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.010   0.001   PHE B 455 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00083 (    4)
  link_NAG-ASN         : angle       1.88059 (   12)
  hydrogen bonds       : bond        0.03977 (  302)
  hydrogen bonds       : angle       4.44717 (  858)
  SS BOND              : bond        0.00341 (    6)
  SS BOND              : angle       1.01923 (   12)
  covalent geometry    : bond        0.00299 ( 6644)
  covalent geometry    : angle       0.51243 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7633 (tp30) cc_final: 0.6753 (tp30)
REVERT: A  225 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6688 (m-30)
REVERT: A  323 MET cc_start: 0.7509 (mtt) cc_final: 0.7305 (mtm)
REVERT: A  347 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8710 (p)
REVERT: A  364 VAL cc_start: 0.8052 (t) cc_final: 0.7763 (t)
REVERT: A  467 GLU cc_start: 0.4571 (OUTLIER) cc_final: 0.3503 (pt0)
REVERT: A  544 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7274 (mt)
REVERT: B  466 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.4790 (ttm170)
REVERT: B  478 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7079 (mtpp)
REVERT: B  500 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8334 (p)
  outliers start: 20
  outliers final: 10
  residues processed: 103
  average time/residue: 0.1804
  time to fit residues: 25.5141
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  467 ASP
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0170
   chunk 65 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.183433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142152 restraints weight = 7322.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.41
r_work: 0.3446 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6654  Z= 0.118
  Angle     :  0.507   7.289   9055  Z= 0.255
  Chirality :  0.041   0.143    954
  Planarity :  0.004   0.043   1166
  Dihedral  :  4.116  23.625    940
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.21 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.30), residues: 786
  helix:  1.77 (0.27), residues: 391
  sheet:  0.67 (0.77), residues: 44
  loop : -1.23 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.010   0.001   PHE B 455 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00094 (    4)
  link_NAG-ASN         : angle       1.84093 (   12)
  hydrogen bonds       : bond        0.03843 (  302)
  hydrogen bonds       : angle       4.36046 (  858)
  SS BOND              : bond        0.00311 (    6)
  SS BOND              : angle       1.06238 (   12)
  covalent geometry    : bond        0.00272 ( 6644)
  covalent geometry    : angle       0.50211 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.663 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7590 (tp30) cc_final: 0.6711 (tp30)
REVERT: A  225 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6487 (m-30)
REVERT: A  347 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8615 (p)
REVERT: A  360 MET cc_start: 0.6837 (ptm) cc_final: 0.6518 (ptm)
REVERT: A  364 VAL cc_start: 0.8000 (t) cc_final: 0.7703 (t)
REVERT: A  544 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7169 (mt)
REVERT: B  466 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.4628 (ttm170)
REVERT: B  478 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6920 (mtpp)
REVERT: B  500 THR cc_start: 0.8507 (p) cc_final: 0.8209 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1729
  time to fit residues: 24.6516
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  478 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0770
   chunk 48 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.182138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.141984 restraints weight = 7308.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.25
r_work: 0.3465 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6654  Z= 0.123
  Angle     :  0.507   7.278   9055  Z= 0.255
  Chirality :  0.041   0.137    954
  Planarity :  0.004   0.044   1166
  Dihedral  :  4.070  23.160    940
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.92 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.30), residues: 786
  helix:  1.80 (0.27), residues: 391
  sheet:  0.67 (0.77), residues: 44
  loop : -1.22 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.009   0.001   PHE B 455 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.003   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    4)
  link_NAG-ASN         : angle       1.70156 (   12)
  hydrogen bonds       : bond        0.03896 (  302)
  hydrogen bonds       : angle       4.36411 (  858)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       1.05808 (   12)
  covalent geometry    : bond        0.00287 ( 6644)
  covalent geometry    : angle       0.50198 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7548 (tp30) cc_final: 0.6725 (tp30)
REVERT: A  225 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6518 (m-30)
REVERT: A  347 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8669 (p)
REVERT: A  360 MET cc_start: 0.6946 (ptm) cc_final: 0.6591 (ptm)
REVERT: A  364 VAL cc_start: 0.8029 (t) cc_final: 0.7720 (t)
REVERT: A  467 GLU cc_start: 0.4542 (OUTLIER) cc_final: 0.3560 (pt0)
REVERT: A  544 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7220 (mt)
REVERT: B  466 ARG cc_start: 0.6575 (OUTLIER) cc_final: 0.4714 (ttm170)
REVERT: B  478 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6881 (mtpp)
REVERT: B  500 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (p)
REVERT: B  508 TYR cc_start: 0.8948 (m-80) cc_final: 0.8584 (m-80)
  outliers start: 17
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1677
  time to fit residues: 23.7531
Evaluate side-chains
  105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0980
   chunk 45 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.183382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143002 restraints weight = 7422.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 2.17
r_work: 0.3442 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6654  Z= 0.124
  Angle     :  0.507   7.301   9055  Z= 0.255
  Chirality :  0.041   0.137    954
  Planarity :  0.004   0.043   1166
  Dihedral  :  4.033  22.889    940
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.06 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.30), residues: 786
  helix:  1.79 (0.27), residues: 391
  sheet:  0.63 (0.77), residues: 44
  loop : -1.22 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.009   0.001   PHE B 455 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    4)
  link_NAG-ASN         : angle       1.65916 (   12)
  hydrogen bonds       : bond        0.03895 (  302)
  hydrogen bonds       : angle       4.36180 (  858)
  SS BOND              : bond        0.00327 (    6)
  SS BOND              : angle       1.03322 (   12)
  covalent geometry    : bond        0.00289 ( 6644)
  covalent geometry    : angle       0.50299 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7543 (tp30) cc_final: 0.6684 (tp30)
REVERT: A  225 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6487 (m-30)
REVERT: A  347 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (p)
REVERT: A  360 MET cc_start: 0.6981 (ptm) cc_final: 0.6645 (ptm)
REVERT: A  364 VAL cc_start: 0.8042 (t) cc_final: 0.7736 (t)
REVERT: A  467 GLU cc_start: 0.4350 (OUTLIER) cc_final: 0.3446 (pt0)
REVERT: A  544 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7171 (mt)
REVERT: B  466 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.4676 (ttm170)
REVERT: B  478 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6936 (mtpp)
REVERT: B  500 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8237 (p)
REVERT: B  508 TYR cc_start: 0.8866 (m-80) cc_final: 0.8555 (m-80)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1689
  time to fit residues: 23.0837
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0970
   chunk 47 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.143364 restraints weight = 7317.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.09
r_work: 0.3459 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6654  Z= 0.115
  Angle     :  0.499   7.413   9055  Z= 0.250
  Chirality :  0.041   0.136    954
  Planarity :  0.003   0.044   1166
  Dihedral  :  3.922  22.045    940
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.63 %
    Favored  : 73.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.31), residues: 786
  helix:  1.84 (0.27), residues: 391
  sheet:  0.04 (0.72), residues: 54
  loop : -1.14 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.011   0.001   PHE A 315 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.004   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00108 (    4)
  link_NAG-ASN         : angle       1.58126 (   12)
  hydrogen bonds       : bond        0.03778 (  302)
  hydrogen bonds       : angle       4.30760 (  858)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       0.96531 (   12)
  covalent geometry    : bond        0.00264 ( 6644)
  covalent geometry    : angle       0.49550 ( 9031)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7582 (tp30) cc_final: 0.6754 (tp30)
REVERT: A  225 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6491 (m-30)
REVERT: A  259 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6644 (pt)
REVERT: A  279 TYR cc_start: 0.7082 (t80) cc_final: 0.6789 (t80)
REVERT: A  347 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8625 (p)
REVERT: A  360 MET cc_start: 0.6874 (ptm) cc_final: 0.6527 (ptm)
REVERT: A  364 VAL cc_start: 0.8062 (t) cc_final: 0.7755 (t)
REVERT: A  467 GLU cc_start: 0.4419 (OUTLIER) cc_final: 0.3547 (pt0)
REVERT: A  510 TYR cc_start: 0.8384 (m-80) cc_final: 0.7881 (m-80)
REVERT: A  544 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7187 (mt)
REVERT: B  338 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7693 (t80)
REVERT: B  466 ARG cc_start: 0.6388 (OUTLIER) cc_final: 0.4623 (ttm170)
REVERT: B  478 LYS cc_start: 0.7108 (OUTLIER) cc_final: 0.6908 (mtpp)
REVERT: B  500 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8206 (p)
REVERT: B  508 TYR cc_start: 0.8822 (m-80) cc_final: 0.8493 (m-80)
  outliers start: 17
  outliers final: 8
  residues processed: 104
  average time/residue: 0.1685
  time to fit residues: 24.6264
Evaluate side-chains
  107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  338 PHE
Chi-restraints excluded: chain B residue  466 ARG
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 11 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 76 optimal weight:    0.2980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.183320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142978 restraints weight = 7477.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.16
r_work: 0.3440 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6654  Z= 0.128
  Angle     :  0.512   7.411   9055  Z= 0.256
  Chirality :  0.041   0.136    954
  Planarity :  0.004   0.044   1166
  Dihedral  :  4.007  22.388    940
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.78 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.31), residues: 786
  helix:  1.79 (0.27), residues: 391
  sheet:  0.02 (0.72), residues: 54
  loop : -1.13 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.010   0.001   PHE B 455 
 TYR   0.021   0.001   TYR A 279 
 ARG   0.003   0.000   ARG A 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    4)
  link_NAG-ASN         : angle       1.55974 (   12)
  hydrogen bonds       : bond        0.03922 (  302)
  hydrogen bonds       : angle       4.35646 (  858)
  SS BOND              : bond        0.00333 (    6)
  SS BOND              : angle       1.04149 (   12)
  covalent geometry    : bond        0.00300 ( 6644)
  covalent geometry    : angle       0.50771 ( 9031)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3558.50 seconds
wall clock time: 62 minutes 21.07 seconds (3741.07 seconds total)