Starting phenix.real_space_refine
on Fri Aug 22 18:06:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dm6_27528/08_2025/8dm6_27528.map"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.016
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    4200      2.51       5
     N    1082      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6559
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1604
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      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
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.18, per 1000 atoms: 0.18
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (79, 86, 122, 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    1240      8.00
     N    1082      7.00
     C    4200      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " 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 A1301 " - " ASN A 343 "
      " NAG D 701 " - " ASN D  53 "
      " NAG D 702 " - " ASN D  90 "
      " NAG D 703 " - " ASN D 103 "
      " NAG D 704 " - " ASN D 322 "
      " NAG D 705 " - " ASN D 432 "
      " NAG D 706 " - " ASN D 546 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 319.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      57.3% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.866A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.572A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 384 through 388'
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.284A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 20 through 53
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 103 through 108
      removed outlier: 4.166A  pdb=" N   VAL D 107 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU D 108 " --> pdb=" O   SER D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
      removed outlier: 3.609A  pdb=" N   SER D 155 " --> pdb=" O   ILE D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 3.807A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 220 through 252
      removed outlier: 4.500A  pdb=" N   GLU D 224 " --> pdb=" O   GLY D 220 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   GLU D 232 " --> pdb=" O   HIS D 228 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 279
      removed outlier: 3.824A  pdb=" N   TYR D 279 " --> pdb=" O   THR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
      removed outlier: 3.744A  pdb=" N   TYR D 385 " --> pdb=" O   TYR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 397 through 413
      removed outlier: 4.340A  pdb=" N   HIS D 401 " --> pdb=" O   ASN D 397 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLU D 402 " --> pdb=" O   GLU D 398 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY D 405 " --> pdb=" O   HIS D 401 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   MET D 408 " --> pdb=" O   VAL D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
      removed outlier: 3.531A  pdb=" N   GLU D 435 " --> pdb=" O   ASP D 431 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 466
      removed outlier: 4.335A  pdb=" N   PHE D 452 " --> pdb=" O   GLY D 448 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 499 through 502
      removed outlier: 3.747A  pdb=" N   SER D 502 " --> pdb=" O   ASP D 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 499 through 502'
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 512 through 533
      removed outlier: 4.372A  pdb=" N   TYR D 516 " --> pdb=" O   PHE D 512 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE D 523 " --> pdb=" O   THR D 519 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 3.992A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 588
    Processing helix  chain 'D' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 6.539A  pdb=" N   ALA A 435 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263
      removed outlier: 5.976A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352
      removed outlier: 6.246A  pdb=" N   ASP D 355 " --> pdb=" O   LEU D 351 " (cutoff:3.500A)

    343 hydrogen bonds defined for protein.
    984 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.74

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2084
        1.35 -     1.48: 1851
        1.48 -     1.61: 2752
        1.61 -     1.73: 0
        1.73 -     1.86: 58
  Bond restraints: 6745
  Sorted by residual:
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.50e+00
  bond pdb=" C1  NAG D 706 "
       pdb=" O5  NAG D 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.52e+00
  bond pdb=" CG  PRO A 330 "
       pdb=" CD  PRO A 330 "
    ideal  model  delta    sigma   weight residual
    1.503  1.575 -0.072 3.40e-02 8.65e+02 4.47e+00
  bond pdb=" C1  NAG D 704 "
       pdb=" O5  NAG D 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" C1  NAG D 702 "
       pdb=" O5  NAG D 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.52e+00
  ... (remaining 6740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 8890
        2.44 -     4.87: 244
        4.87 -     7.31: 21
        7.31 -     9.74: 7
        9.74 -    12.18: 4
  Bond angle restraints: 9166
  Sorted by residual:
  angle pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
        pdb=" C   ALA A 372 "
      ideal   model   delta    sigma   weight residual
     109.81  120.82  -11.01 2.21e+00 2.05e-01 2.48e+01
  angle pdb=" CA  CYS A 391 "
        pdb=" CB  CYS A 391 "
        pdb=" SG  CYS A 391 "
      ideal   model   delta    sigma   weight residual
     114.40  125.13  -10.73 2.30e+00 1.89e-01 2.18e+01
  angle pdb=" CB  MET D 152 "
        pdb=" CG  MET D 152 "
        pdb=" SD  MET D 152 "
      ideal   model   delta    sigma   weight residual
     112.70  124.88  -12.18 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" CB  LYS D 534 "
        pdb=" CG  LYS D 534 "
        pdb=" CD  LYS D 534 "
      ideal   model   delta    sigma   weight residual
     111.30  120.35   -9.05 2.30e+00 1.89e-01 1.55e+01
  angle pdb=" CA  PRO A 330 "
        pdb=" N   PRO A 330 "
        pdb=" CD  PRO A 330 "
      ideal   model   delta    sigma   weight residual
     112.00  106.58    5.42 1.40e+00 5.10e-01 1.50e+01
  ... (remaining 9161 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 3648
       17.48 -    34.97: 340
       34.97 -    52.45: 60
       52.45 -    69.94: 14
       69.94 -    87.42: 8
  Dihedral angle restraints: 4070
    sinusoidal: 1733
      harmonic: 2337
  Sorted by residual:
  dihedral pdb=" CB  CYS D 133 "
           pdb=" SG  CYS D 133 "
           pdb=" SG  CYS D 141 "
           pdb=" CB  CYS D 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.29   54.71     1      1.00e+01 1.00e-02 4.05e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.17   37.83     1      1.00e+01 1.00e-02 2.02e+01
  dihedral pdb=" CA  CYS A 391 "
           pdb=" C   CYS A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.69  -16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4067 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 588
       0.046 -    0.093: 273
       0.093 -    0.139: 86
       0.139 -    0.185: 24
       0.185 -    0.231: 5
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" CA  ASN A 360 "
            pdb=" N   ASN A 360 "
            pdb=" C   ASN A 360 "
            pdb=" CB  ASN A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CG  LEU D 267 "
            pdb=" CB  LEU D 267 "
            pdb=" CD1 LEU D 267 "
            pdb=" CD2 LEU D 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  THR A 333 "
            pdb=" CA  THR A 333 "
            pdb=" OG1 THR A 333 "
            pdb=" CG2 THR A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 973 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS D 241 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.90e+00
        pdb=" C   HIS D 241 "    0.054 2.00e-02 2.50e+03
        pdb=" O   HIS D 241 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ALA D 242 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 244 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.52e+00
        pdb=" C   VAL D 244 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL D 244 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ARG D 245 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 226 "   -0.015 2.00e-02 2.50e+03   2.91e-02 8.45e+00
        pdb=" C   VAL D 226 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL D 226 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU D 227 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 1832
        2.81 -     3.33: 5953
        3.33 -     3.85: 11478
        3.85 -     4.38: 13089
        4.38 -     4.90: 22516
  Nonbonded interactions: 54868
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 183 "
            pdb=" OD1 ASP D 509 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OE2 GLU D 435 "
            pdb=" NZ  LYS D 541 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" OE1 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OD1 ASP D 382 "
            pdb=" OH  TYR D 385 "
     model   vdw
     2.360 3.040
  ... (remaining 54863 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:             5.550
  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:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
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      :  0.006   0.072   6758  Z= 0.276
  Angle     :  0.948  12.179   9199  Z= 0.513
  Chirality :  0.059   0.231    976
  Planarity :  0.007   0.063   1179
  Dihedral  : 14.081  87.420   2552
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  4.29 %
    Favored  : 95.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.27), residues: 792
  helix:  0.27 (0.23), residues: 389
  sheet:  2.01 (0.81), residues: 34
  loop : -0.50 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 457 
 TYR   0.031   0.002   TYR D 385 
 PHE   0.024   0.003   PHE A 377 
 TRP   0.019   0.002   TRP D 594 
 HIS   0.007   0.002   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 6745)
  covalent geometry    : angle       0.93686 ( 9166)
  SS BOND              : bond        0.00805 (    6)
  SS BOND              : angle       2.14270 (   12)
  hydrogen bonds       : bond        0.14801 (  321)
  hydrogen bonds       : angle       6.64435 (  984)
  link_NAG-ASN         : bond        0.00496 (    7)
  link_NAG-ASN         : angle       2.86529 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 190
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7820 (ttt90)
REVERT: A  465 GLU cc_start: 0.8263 (tt0) cc_final: 0.8028 (tt0)
REVERT: D   55 THR cc_start: 0.8054 (m) cc_final: 0.7795 (p)
REVERT: D  270 MET cc_start: 0.8145 (tpt) cc_final: 0.7927 (tpp)
REVERT: D  366 MET cc_start: 0.8582 (ttp) cc_final: 0.8362 (ttp)
REVERT: D  483 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: D  534 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8302 (mmtm)
REVERT: D  582 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (mmm160)
REVERT: D  603 PHE cc_start: 0.8656 (t80) cc_final: 0.8027 (t80)
REVERT: D  604 VAL cc_start: 0.9243 (p) cc_final: 0.8911 (t)
  outliers start: 4
  outliers final: 1
  residues processed: 192
  average time/residue: 0.4943
  time to fit residues: 99.0636
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
D  42 GLN
D  76 GLN
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 175 GLN
D 374 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.102680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.079940 restraints weight = 12252.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.83
r_work: 0.2980 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6758  Z= 0.163
  Angle     :  0.619   7.466   9199  Z= 0.316
  Chirality :  0.044   0.190    976
  Planarity :  0.005   0.036   1179
  Dihedral  :  5.819  53.847   1014
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.59 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.28), residues: 792
  helix:  1.02 (0.25), residues: 401
  sheet:  1.21 (0.74), residues: 43
  loop : -0.12 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 582 
 TYR   0.015   0.001   TYR D  41 
 PHE   0.014   0.001   PHE D 369 
 TRP   0.017   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6745)
  covalent geometry    : angle       0.60646 ( 9166)
  SS BOND              : bond        0.00520 (    6)
  SS BOND              : angle       1.33992 (   12)
  hydrogen bonds       : bond        0.05265 (  321)
  hydrogen bonds       : angle       5.04720 (  984)
  link_NAG-ASN         : bond        0.00345 (    7)
  link_NAG-ASN         : angle       2.45432 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 ASP cc_start: 0.8133 (p0) cc_final: 0.7810 (p0)
REVERT: A  340 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8669 (mp0)
REVERT: A  357 ARG cc_start: 0.8773 (ptm160) cc_final: 0.8229 (ttt90)
REVERT: A  465 GLU cc_start: 0.8597 (tt0) cc_final: 0.8213 (tt0)
REVERT: D   23 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8472 (pt0)
REVERT: D   26 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8333 (mtmm)
REVERT: D   55 THR cc_start: 0.7995 (m) cc_final: 0.7622 (p)
REVERT: D  182 GLU cc_start: 0.8550 (tt0) cc_final: 0.8128 (tt0)
REVERT: D  228 HIS cc_start: 0.8445 (t70) cc_final: 0.7972 (m90)
REVERT: D  270 MET cc_start: 0.8224 (tpt) cc_final: 0.7907 (tpp)
REVERT: D  287 GLN cc_start: 0.8689 (mp10) cc_final: 0.8259 (pm20)
REVERT: D  408 MET cc_start: 0.9221 (mmt) cc_final: 0.8954 (mmt)
REVERT: D  429 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8120 (mm-40)
REVERT: D  467 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7701 (mp0)
REVERT: D  470 LYS cc_start: 0.8762 (tppp) cc_final: 0.8557 (tppp)
REVERT: D  472 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7996 (mm-40)
REVERT: D  483 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: D  497 TYR cc_start: 0.8809 (m-80) cc_final: 0.8564 (m-80)
REVERT: D  603 PHE cc_start: 0.8728 (t80) cc_final: 0.8293 (t80)
  outliers start: 17
  outliers final: 4
  residues processed: 124
  average time/residue: 0.5063
  time to fit residues: 65.4809
Evaluate side-chains
  110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain D residue  429 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
D 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.098349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.075491 restraints weight = 12239.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.86
r_work: 0.2883 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6758  Z= 0.239
  Angle     :  0.644  11.052   9199  Z= 0.323
  Chirality :  0.045   0.332    976
  Planarity :  0.004   0.034   1179
  Dihedral  :  5.288  40.679   1012
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.59 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.29), residues: 792
  helix:  1.16 (0.25), residues: 409
  sheet:  0.95 (0.77), residues: 43
  loop :  0.17 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 466 
 TYR   0.016   0.002   TYR D 385 
 PHE   0.022   0.002   PHE D 400 
 TRP   0.013   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00543 ( 6745)
  covalent geometry    : angle       0.62416 ( 9166)
  SS BOND              : bond        0.00547 (    6)
  SS BOND              : angle       1.26232 (   12)
  hydrogen bonds       : bond        0.05417 (  321)
  hydrogen bonds       : angle       4.91819 (  984)
  link_NAG-ASN         : bond        0.00824 (    7)
  link_NAG-ASN         : angle       3.23353 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 ASP cc_start: 0.8390 (p0) cc_final: 0.7886 (p0)
REVERT: A  340 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8712 (mp0)
REVERT: A  465 GLU cc_start: 0.8670 (tt0) cc_final: 0.8388 (tt0)
REVERT: D   26 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8340 (mttm)
REVERT: D   55 THR cc_start: 0.8107 (m) cc_final: 0.7823 (p)
REVERT: D  115 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8173 (tpm170)
REVERT: D  182 GLU cc_start: 0.8680 (tt0) cc_final: 0.8351 (tt0)
REVERT: D  228 HIS cc_start: 0.8345 (t70) cc_final: 0.8144 (t70)
REVERT: D  243 TYR cc_start: 0.9023 (t80) cc_final: 0.8807 (t80)
REVERT: D  287 GLN cc_start: 0.8703 (mp10) cc_final: 0.8222 (pm20)
REVERT: D  470 LYS cc_start: 0.8712 (tppp) cc_final: 0.8458 (tppp)
REVERT: D  483 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D  497 TYR cc_start: 0.8854 (m-80) cc_final: 0.8628 (m-80)
REVERT: D  603 PHE cc_start: 0.8796 (t80) cc_final: 0.8391 (t80)
  outliers start: 26
  outliers final: 12
  residues processed: 119
  average time/residue: 0.5202
  time to fit residues: 64.5599
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  143 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  429 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.077430 restraints weight = 12314.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.85
r_work: 0.2919 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6758  Z= 0.158
  Angle     :  0.574   6.436   9199  Z= 0.288
  Chirality :  0.042   0.198    976
  Planarity :  0.004   0.032   1179
  Dihedral  :  4.529  28.369   1012
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.45 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.30), residues: 792
  helix:  1.35 (0.26), residues: 408
  sheet:  0.29 (0.69), residues: 53
  loop :  0.36 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.014   0.001   TYR D  50 
 PHE   0.013   0.001   PHE D 369 
 TRP   0.015   0.001   TRP D 168 
 HIS   0.003   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 6745)
  covalent geometry    : angle       0.56790 ( 9166)
  SS BOND              : bond        0.00544 (    6)
  SS BOND              : angle       1.17591 (   12)
  hydrogen bonds       : bond        0.04813 (  321)
  hydrogen bonds       : angle       4.68322 (  984)
  link_NAG-ASN         : bond        0.00217 (    7)
  link_NAG-ASN         : angle       1.70256 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7419 (ppp-140)
REVERT: A  465 GLU cc_start: 0.8685 (tt0) cc_final: 0.8362 (tt0)
REVERT: D   26 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8351 (mttm)
REVERT: D   55 THR cc_start: 0.8167 (m) cc_final: 0.7890 (p)
REVERT: D  115 ARG cc_start: 0.8625 (tpm-80) cc_final: 0.8246 (tpm170)
REVERT: D  152 MET cc_start: 0.8792 (mmm) cc_final: 0.8409 (mmm)
REVERT: D  182 GLU cc_start: 0.8692 (tt0) cc_final: 0.8357 (tt0)
REVERT: D  213 ASP cc_start: 0.9094 (t70) cc_final: 0.8733 (t0)
REVERT: D  243 TYR cc_start: 0.9023 (t80) cc_final: 0.8819 (t80)
REVERT: D  287 GLN cc_start: 0.8683 (mp10) cc_final: 0.8216 (pm20)
REVERT: D  305 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8479 (tm-30)
REVERT: D  467 GLU cc_start: 0.8411 (mp0) cc_final: 0.7666 (mp0)
REVERT: D  470 LYS cc_start: 0.8742 (tppp) cc_final: 0.8460 (tppp)
REVERT: D  479 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8424 (mt-10)
REVERT: D  483 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8334 (tm-30)
REVERT: D  531 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8318 (mt0)
REVERT: D  582 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.7782 (mmm160)
REVERT: D  596 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8823 (mtmm)
REVERT: D  603 PHE cc_start: 0.8833 (t80) cc_final: 0.8396 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 117
  average time/residue: 0.4848
  time to fit residues: 59.3248
Evaluate side-chains
  111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  378 LYS
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  143 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  305 GLN
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  429 GLN
Chi-restraints excluded: chain D residue  531 GLN
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0870
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
A 477 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.100728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.077926 restraints weight = 12274.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 2.81
r_work: 0.2911 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6758  Z= 0.143
  Angle     :  0.566   6.947   9199  Z= 0.282
  Chirality :  0.042   0.158    976
  Planarity :  0.003   0.031   1179
  Dihedral  :  4.275  25.752   1012
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.88 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.29), residues: 792
  helix:  1.54 (0.26), residues: 402
  sheet:  0.87 (0.76), residues: 43
  loop :  0.24 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.013   0.001   TYR D  50 
 PHE   0.013   0.001   PHE D 369 
 TRP   0.012   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6745)
  covalent geometry    : angle       0.56099 ( 9166)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.19097 (   12)
  hydrogen bonds       : bond        0.04644 (  321)
  hydrogen bonds       : angle       4.59801 (  984)
  link_NAG-ASN         : bond        0.00197 (    7)
  link_NAG-ASN         : angle       1.44808 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8727 (mp0)
REVERT: A  465 GLU cc_start: 0.8698 (tt0) cc_final: 0.8397 (tt0)
REVERT: A  500 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9025 (p)
REVERT: D   26 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8357 (mttm)
REVERT: D   55 THR cc_start: 0.8163 (m) cc_final: 0.7853 (p)
REVERT: D  115 ARG cc_start: 0.8670 (tpm-80) cc_final: 0.8307 (tpm170)
REVERT: D  182 GLU cc_start: 0.8723 (tt0) cc_final: 0.8355 (tt0)
REVERT: D  243 TYR cc_start: 0.8982 (t80) cc_final: 0.8753 (t80)
REVERT: D  287 GLN cc_start: 0.8687 (mp10) cc_final: 0.8213 (pm20)
REVERT: D  467 GLU cc_start: 0.8378 (mp0) cc_final: 0.7594 (mp0)
REVERT: D  470 LYS cc_start: 0.8735 (tppp) cc_final: 0.8497 (tppp)
REVERT: D  479 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: D  483 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D  497 TYR cc_start: 0.8786 (m-80) cc_final: 0.8525 (m-80)
REVERT: D  531 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8329 (mt0)
REVERT: D  596 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8743 (mtmm)
REVERT: D  603 PHE cc_start: 0.8823 (t80) cc_final: 0.8397 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 116
  average time/residue: 0.5038
  time to fit residues: 61.2331
Evaluate side-chains
  115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  429 GLN
Chi-restraints excluded: chain D residue  531 GLN
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0040
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.3992

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.101708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.078810 restraints weight = 12199.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.80
r_work: 0.2928 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6758  Z= 0.122
  Angle     :  0.539   7.488   9199  Z= 0.267
  Chirality :  0.041   0.155    976
  Planarity :  0.003   0.030   1179
  Dihedral  :  4.037  24.173   1012
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.45 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.30), residues: 792
  helix:  1.59 (0.26), residues: 411
  sheet:  0.77 (0.75), residues: 43
  loop :  0.23 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 306 
 TYR   0.012   0.001   TYR D  50 
 PHE   0.013   0.001   PHE D 369 
 TRP   0.011   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 6745)
  covalent geometry    : angle       0.53494 ( 9166)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       1.03524 (   12)
  hydrogen bonds       : bond        0.04389 (  321)
  hydrogen bonds       : angle       4.49630 (  984)
  link_NAG-ASN         : bond        0.00218 (    7)
  link_NAG-ASN         : angle       1.39814 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.8660 (ptm160) cc_final: 0.8093 (ttt90)
REVERT: A  405 ASN cc_start: 0.8881 (m-40) cc_final: 0.8625 (m110)
REVERT: A  465 GLU cc_start: 0.8697 (tt0) cc_final: 0.8337 (tt0)
REVERT: A  500 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9028 (p)
REVERT: D   26 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8333 (mttm)
REVERT: D  213 ASP cc_start: 0.9074 (t70) cc_final: 0.8717 (t0)
REVERT: D  243 TYR cc_start: 0.8946 (t80) cc_final: 0.8718 (t80)
REVERT: D  287 GLN cc_start: 0.8695 (mp10) cc_final: 0.8233 (pm20)
REVERT: D  467 GLU cc_start: 0.8402 (mp0) cc_final: 0.7619 (mp0)
REVERT: D  470 LYS cc_start: 0.8725 (tppp) cc_final: 0.8472 (tppp)
REVERT: D  472 GLN cc_start: 0.8220 (mm-40) cc_final: 0.8007 (mm-40)
REVERT: D  479 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8306 (mt-10)
REVERT: D  483 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8304 (tm-30)
REVERT: D  596 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8737 (mtmm)
REVERT: D  603 PHE cc_start: 0.8832 (t80) cc_final: 0.8392 (t80)
  outliers start: 23
  outliers final: 11
  residues processed: 122
  average time/residue: 0.4801
  time to fit residues: 61.3761
Evaluate side-chains
  112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  143 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  429 GLN
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.2980
   chunk 60 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.077440 restraints weight = 12056.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.80
r_work: 0.2908 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6758  Z= 0.150
  Angle     :  0.571   7.903   9199  Z= 0.282
  Chirality :  0.042   0.156    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.090  24.974   1012
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.74 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.30), residues: 792
  helix:  1.66 (0.26), residues: 403
  sheet:  0.75 (0.75), residues: 43
  loop :  0.27 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 493 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.014   0.001   PHE D 369 
 TRP   0.011   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6745)
  covalent geometry    : angle       0.56632 ( 9166)
  SS BOND              : bond        0.00484 (    6)
  SS BOND              : angle       1.05328 (   12)
  hydrogen bonds       : bond        0.04582 (  321)
  hydrogen bonds       : angle       4.52076 (  984)
  link_NAG-ASN         : bond        0.00199 (    7)
  link_NAG-ASN         : angle       1.43627 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 GLU cc_start: 0.8690 (tt0) cc_final: 0.8335 (tt0)
REVERT: A  500 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9009 (p)
REVERT: D   26 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8337 (mttp)
REVERT: D  114 LYS cc_start: 0.9461 (pptt) cc_final: 0.9255 (tmmt)
REVERT: D  213 ASP cc_start: 0.9077 (t70) cc_final: 0.8725 (t0)
REVERT: D  243 TYR cc_start: 0.8986 (t80) cc_final: 0.8753 (t80)
REVERT: D  287 GLN cc_start: 0.8665 (mp10) cc_final: 0.8203 (pm20)
REVERT: D  467 GLU cc_start: 0.8378 (mp0) cc_final: 0.7590 (mp0)
REVERT: D  470 LYS cc_start: 0.8765 (tppp) cc_final: 0.8488 (tppp)
REVERT: D  483 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: D  497 TYR cc_start: 0.8725 (m-80) cc_final: 0.8113 (m-80)
REVERT: D  582 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8095 (mmm160)
REVERT: D  596 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8728 (mtmm)
REVERT: D  603 PHE cc_start: 0.8823 (t80) cc_final: 0.8380 (t80)
  outliers start: 21
  outliers final: 11
  residues processed: 114
  average time/residue: 0.4943
  time to fit residues: 59.1922
Evaluate side-chains
  109 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  429 GLN
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.099766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.076757 restraints weight = 12220.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.85
r_work: 0.2911 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6758  Z= 0.154
  Angle     :  0.571   8.325   9199  Z= 0.284
  Chirality :  0.042   0.153    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.122  24.946   1012
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.89 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.29), residues: 792
  helix:  1.64 (0.26), residues: 403
  sheet:  0.77 (0.75), residues: 43
  loop :  0.22 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.011   0.001   TYR D  41 
 PHE   0.019   0.001   PHE A 375 
 TRP   0.011   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6745)
  covalent geometry    : angle       0.56671 ( 9166)
  SS BOND              : bond        0.00495 (    6)
  SS BOND              : angle       1.09123 (   12)
  hydrogen bonds       : bond        0.04609 (  321)
  hydrogen bonds       : angle       4.52344 (  984)
  link_NAG-ASN         : bond        0.00197 (    7)
  link_NAG-ASN         : angle       1.43661 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 GLU cc_start: 0.8666 (tt0) cc_final: 0.8301 (tt0)
REVERT: A  500 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8941 (p)
REVERT: D   26 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8223 (mttm)
REVERT: D   86 GLN cc_start: 0.8581 (pp30) cc_final: 0.8336 (tm-30)
REVERT: D  213 ASP cc_start: 0.9079 (t70) cc_final: 0.8721 (t0)
REVERT: D  287 GLN cc_start: 0.8676 (mp10) cc_final: 0.8218 (pm20)
REVERT: D  467 GLU cc_start: 0.8338 (mp0) cc_final: 0.7509 (mp0)
REVERT: D  470 LYS cc_start: 0.8711 (tppp) cc_final: 0.8418 (tppp)
REVERT: D  472 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7926 (mm-40)
REVERT: D  479 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8195 (mt-10)
REVERT: D  483 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8280 (tm-30)
REVERT: D  497 TYR cc_start: 0.8635 (m-80) cc_final: 0.8208 (m-80)
REVERT: D  582 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8009 (mmm160)
REVERT: D  596 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8607 (mtmm)
REVERT: D  603 PHE cc_start: 0.8766 (t80) cc_final: 0.8289 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 108
  average time/residue: 0.5104
  time to fit residues: 57.7254
Evaluate side-chains
  108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  143 LEU
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 58 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.098596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.075397 restraints weight = 12325.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 2.86
r_work: 0.2882 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6758  Z= 0.185
  Angle     :  0.621   8.666   9199  Z= 0.307
  Chirality :  0.043   0.157    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.249  24.507   1012
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.60 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.30), residues: 792
  helix:  1.49 (0.26), residues: 410
  sheet:  0.52 (0.74), residues: 48
  loop :  0.34 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.013   0.001   TYR D 385 
 PHE   0.019   0.001   PHE A 375 
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 6745)
  covalent geometry    : angle       0.61631 ( 9166)
  SS BOND              : bond        0.00508 (    6)
  SS BOND              : angle       1.09414 (   12)
  hydrogen bonds       : bond        0.04831 (  321)
  hydrogen bonds       : angle       4.58646 (  984)
  link_NAG-ASN         : bond        0.00189 (    7)
  link_NAG-ASN         : angle       1.52975 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7783 (ppp-140)
REVERT: A  465 GLU cc_start: 0.8694 (tt0) cc_final: 0.8384 (tt0)
REVERT: A  500 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9057 (p)
REVERT: D   26 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8227 (mttm)
REVERT: D  114 LYS cc_start: 0.9464 (pptt) cc_final: 0.9254 (tmmt)
REVERT: D  213 ASP cc_start: 0.9086 (t70) cc_final: 0.8729 (t0)
REVERT: D  287 GLN cc_start: 0.8726 (mp10) cc_final: 0.8312 (pm20)
REVERT: D  467 GLU cc_start: 0.8328 (mp0) cc_final: 0.7501 (mp0)
REVERT: D  470 LYS cc_start: 0.8716 (tppp) cc_final: 0.8478 (tppp)
REVERT: D  472 GLN cc_start: 0.8218 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: D  483 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: D  497 TYR cc_start: 0.8680 (m-80) cc_final: 0.8198 (m-80)
REVERT: D  582 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8022 (mmm160)
REVERT: D  596 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8674 (mtmm)
REVERT: D  603 PHE cc_start: 0.8766 (t80) cc_final: 0.8329 (t80)
  outliers start: 16
  outliers final: 9
  residues processed: 106
  average time/residue: 0.5095
  time to fit residues: 56.6556
Evaluate side-chains
  107 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  596 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  89 GLN
D 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.099032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.076006 restraints weight = 12244.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 2.83
r_work: 0.2895 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6758  Z= 0.168
  Angle     :  0.618   8.488   9199  Z= 0.305
  Chirality :  0.043   0.152    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.209  24.388   1012
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.74 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.30), residues: 792
  helix:  1.44 (0.25), residues: 410
  sheet:  0.53 (0.75), residues: 48
  loop :  0.34 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 466 
 TYR   0.011   0.001   TYR D 243 
 PHE   0.019   0.001   PHE A 375 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6745)
  covalent geometry    : angle       0.61406 ( 9166)
  SS BOND              : bond        0.00510 (    6)
  SS BOND              : angle       1.06747 (   12)
  hydrogen bonds       : bond        0.04696 (  321)
  hydrogen bonds       : angle       4.58190 (  984)
  link_NAG-ASN         : bond        0.00211 (    7)
  link_NAG-ASN         : angle       1.47334 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7761 (ppp-140)
REVERT: A  465 GLU cc_start: 0.8704 (tt0) cc_final: 0.8399 (tt0)
REVERT: D   26 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8228 (mttm)
REVERT: D   86 GLN cc_start: 0.8588 (pp30) cc_final: 0.7571 (pp30)
REVERT: D  213 ASP cc_start: 0.9083 (t70) cc_final: 0.8741 (t0)
REVERT: D  287 GLN cc_start: 0.8739 (mp10) cc_final: 0.8329 (pm20)
REVERT: D  467 GLU cc_start: 0.8321 (mp0) cc_final: 0.7485 (mp0)
REVERT: D  470 LYS cc_start: 0.8703 (tppp) cc_final: 0.8468 (tppp)
REVERT: D  472 GLN cc_start: 0.8251 (mm-40) cc_final: 0.8041 (mm-40)
REVERT: D  479 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8251 (mt-10)
REVERT: D  483 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: D  497 TYR cc_start: 0.8678 (m-80) cc_final: 0.8185 (m-80)
REVERT: D  582 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.8040 (mmm160)
REVERT: D  603 PHE cc_start: 0.8765 (t80) cc_final: 0.8331 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 0.5270
  time to fit residues: 57.4081
Evaluate side-chains
  102 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  503 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.099361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.076453 restraints weight = 12179.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.79
r_work: 0.2903 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6758  Z= 0.159
  Angle     :  0.637  12.216   9199  Z= 0.311
  Chirality :  0.042   0.155    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.218  24.745   1012
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.46 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.30), residues: 792
  helix:  1.44 (0.26), residues: 410
  sheet:  0.55 (0.75), residues: 48
  loop :  0.36 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 493 
 TYR   0.012   0.001   TYR D 243 
 PHE   0.018   0.001   PHE A 375 
 TRP   0.009   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6745)
  covalent geometry    : angle       0.63327 ( 9166)
  SS BOND              : bond        0.00472 (    6)
  SS BOND              : angle       1.05594 (   12)
  hydrogen bonds       : bond        0.04644 (  321)
  hydrogen bonds       : angle       4.57043 (  984)
  link_NAG-ASN         : bond        0.00204 (    7)
  link_NAG-ASN         : angle       1.51199 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2025.03 seconds
wall clock time: 35 minutes 11.00 seconds (2111.00 seconds total)