Starting phenix.real_space_refine
on Thu Jul 24 21:49:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dm6_27528/07_2025/8dm6_27528.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dm6_27528/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2025/8dm6_27528.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2025/8dm6_27528.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2025/8dm6_27528.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dm6_27528/07_2025/8dm6_27528.cif"
  }
  resolution = 2.77
  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=   0.016
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.32, per 1000 atoms: 0.81
  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: 1.52
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.71
  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: 1.90

  Time building geometry restraints manager: 1.86 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:             5.800
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.520
  Find NCS groups from input model:        0.070
  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:16.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.580
-------------------------------------------------------------------------------
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 (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: -0.08 (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
 TRP   0.019   0.002   TRP D 594 
 HIS   0.007   0.002   HIS A 505 
 PHE   0.024   0.003   PHE A 377 
 TYR   0.031   0.002   TYR D 385 
 ARG   0.012   0.001   ARG A 457 

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

*********************** 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  : 1.137 
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: 0.7796 (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: 1.3040
  time to fit residues: 261.8681
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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 66 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0470
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.102761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.080202 restraints weight = 12126.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.79
r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6758  Z= 0.160
  Angle     :  0.614   8.060   9199  Z= 0.313
  Chirality :  0.044   0.274    976
  Planarity :  0.005   0.036   1179
  Dihedral  :  5.662  53.377   1014
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.88 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.29), residues: 792
  helix:  1.04 (0.25), residues: 402
  sheet:  1.21 (0.75), residues: 43
  loop : -0.07 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.013   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D  41 
 ARG   0.004   0.000   ARG D 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (    7)
  link_NAG-ASN         : angle       2.23885 (   21)
  hydrogen bonds       : bond        0.05069 (  321)
  hydrogen bonds       : angle       4.99414 (  984)
  SS BOND              : bond        0.00525 (    6)
  SS BOND              : angle       1.35262 (   12)
  covalent geometry    : bond        0.00352 ( 6745)
  covalent geometry    : angle       0.60410 ( 9166)

*********************** 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
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 ASP cc_start: 0.8089 (p0) cc_final: 0.7760 (p0)
REVERT: A  340 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8688 (mp0)
REVERT: A  357 ARG cc_start: 0.8777 (ptm160) cc_final: 0.8275 (ttt90)
REVERT: A  465 GLU cc_start: 0.8595 (tt0) cc_final: 0.8211 (tt0)
REVERT: D   26 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8334 (mtmm)
REVERT: D   55 THR cc_start: 0.8071 (m) cc_final: 0.7691 (p)
REVERT: D  182 GLU cc_start: 0.8556 (tt0) cc_final: 0.8160 (tt0)
REVERT: D  228 HIS cc_start: 0.8435 (t70) cc_final: 0.7962 (m90)
REVERT: D  270 MET cc_start: 0.8222 (tpt) cc_final: 0.7930 (tpp)
REVERT: D  287 GLN cc_start: 0.8692 (mp10) cc_final: 0.8264 (pm20)
REVERT: D  408 MET cc_start: 0.9222 (mmt) cc_final: 0.8949 (mmt)
REVERT: D  429 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8155 (mm-40)
REVERT: D  467 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7701 (mp0)
REVERT: D  470 LYS cc_start: 0.8779 (tppp) cc_final: 0.8573 (tppp)
REVERT: D  472 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8060 (mm-40)
REVERT: D  483 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: D  497 TYR cc_start: 0.8809 (m-80) cc_final: 0.8521 (m-80)
REVERT: D  582 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8184 (mmm160)
REVERT: D  603 PHE cc_start: 0.8740 (t80) cc_final: 0.8321 (t80)
  outliers start: 17
  outliers final: 4
  residues processed: 125
  average time/residue: 1.4266
  time to fit residues: 186.3476
Evaluate side-chains
  115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  429 GLN
Chi-restraints excluded: chain D residue  549 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.100762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.078012 restraints weight = 12285.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.85
r_work: 0.2923 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6758  Z= 0.165
  Angle     :  0.579   7.461   9199  Z= 0.292
  Chirality :  0.043   0.244    976
  Planarity :  0.004   0.034   1179
  Dihedral  :  4.997  44.938   1012
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.31 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.29), residues: 792
  helix:  1.24 (0.25), residues: 408
  sheet:  2.09 (0.87), residues: 33
  loop :  0.07 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 165 
 HIS   0.002   0.001   HIS D 535 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.016   0.001   TYR D  50 
 ARG   0.004   0.000   ARG D 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00315 (    7)
  link_NAG-ASN         : angle       2.46039 (   21)
  hydrogen bonds       : bond        0.04947 (  321)
  hydrogen bonds       : angle       4.79046 (  984)
  SS BOND              : bond        0.00508 (    6)
  SS BOND              : angle       1.17601 (   12)
  covalent geometry    : bond        0.00371 ( 6745)
  covalent geometry    : angle       0.56672 ( 9166)

*********************** 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
  136 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 ASP cc_start: 0.8362 (p0) cc_final: 0.7814 (p0)
REVERT: A  340 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8653 (mp0)
REVERT: A  357 ARG cc_start: 0.8759 (ptm160) cc_final: 0.8234 (ttt90)
REVERT: A  465 GLU cc_start: 0.8648 (tt0) cc_final: 0.8348 (tt0)
REVERT: D   26 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8324 (mttm)
REVERT: D   55 THR cc_start: 0.8045 (m) cc_final: 0.7661 (p)
REVERT: D  115 ARG cc_start: 0.8547 (tpm-80) cc_final: 0.8023 (tpm170)
REVERT: D  182 GLU cc_start: 0.8621 (tt0) cc_final: 0.8273 (tt0)
REVERT: D  243 TYR cc_start: 0.8895 (t80) cc_final: 0.8678 (t80)
REVERT: D  270 MET cc_start: 0.8232 (tpt) cc_final: 0.7927 (tpp)
REVERT: D  287 GLN cc_start: 0.8675 (mp10) cc_final: 0.8172 (pm20)
REVERT: D  305 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (tm-30)
REVERT: D  408 MET cc_start: 0.9222 (mmt) cc_final: 0.9008 (mmt)
REVERT: D  470 LYS cc_start: 0.8706 (tppp) cc_final: 0.8450 (tppp)
REVERT: D  483 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: D  582 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8214 (mmm160)
REVERT: D  603 PHE cc_start: 0.8784 (t80) cc_final: 0.8327 (t80)
  outliers start: 22
  outliers final: 8
  residues processed: 126
  average time/residue: 1.3250
  time to fit residues: 174.9792
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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  503 VAL
Chi-restraints excluded: chain D residue  124 SER
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  305 GLN
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 27 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0870
   chunk 49 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
D 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.101394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.078481 restraints weight = 12378.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 2.89
r_work: 0.2941 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6758  Z= 0.142
  Angle     :  0.555   6.619   9199  Z= 0.280
  Chirality :  0.042   0.191    976
  Planarity :  0.004   0.030   1179
  Dihedral  :  4.368  27.643   1012
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.74 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 792
  helix:  1.41 (0.26), residues: 408
  sheet:  2.12 (0.89), residues: 33
  loop :  0.22 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 168 
 HIS   0.003   0.001   HIS D 239 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.015   0.001   TYR D  50 
 ARG   0.002   0.000   ARG D 306 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    7)
  link_NAG-ASN         : angle       1.55807 (   21)
  hydrogen bonds       : bond        0.04661 (  321)
  hydrogen bonds       : angle       4.61091 (  984)
  SS BOND              : bond        0.00507 (    6)
  SS BOND              : angle       1.16077 (   12)
  covalent geometry    : bond        0.00316 ( 6745)
  covalent geometry    : angle       0.54977 ( 9166)

*********************** 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: 22
    poor density    : 104
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 ARG cc_start: 0.8761 (ptm160) cc_final: 0.8176 (ttt90)
REVERT: A  465 GLU cc_start: 0.8668 (tt0) cc_final: 0.8326 (tt0)
REVERT: A  500 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9022 (p)
REVERT: D   26 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8329 (mttp)
REVERT: D  115 ARG cc_start: 0.8629 (tpm-80) cc_final: 0.8196 (tpm170)
REVERT: D  182 GLU cc_start: 0.8679 (tt0) cc_final: 0.8335 (tt0)
REVERT: D  243 TYR cc_start: 0.8937 (t80) cc_final: 0.8731 (t80)
REVERT: D  270 MET cc_start: 0.8179 (tpt) cc_final: 0.7901 (tpp)
REVERT: D  287 GLN cc_start: 0.8670 (mp10) cc_final: 0.8180 (pm20)
REVERT: D  467 GLU cc_start: 0.8298 (mp0) cc_final: 0.7534 (mp0)
REVERT: D  470 LYS cc_start: 0.8755 (tppp) cc_final: 0.8531 (tppp)
REVERT: D  479 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: D  483 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: D  531 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8319 (mt0)
REVERT: D  582 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8211 (mmm160)
REVERT: D  603 PHE cc_start: 0.8803 (t80) cc_final: 0.8364 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 118
  average time/residue: 1.3890
  time to fit residues: 171.5071
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0570
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 52 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 477 ASN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.100523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.077366 restraints weight = 12159.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 2.86
r_work: 0.2919 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6758  Z= 0.161
  Angle     :  0.564   6.793   9199  Z= 0.283
  Chirality :  0.042   0.165    976
  Planarity :  0.004   0.030   1179
  Dihedral  :  4.275  26.115   1012
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.30), residues: 792
  helix:  1.50 (0.26), residues: 409
  sheet:  1.98 (0.88), residues: 33
  loop :  0.27 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 535 
 PHE   0.015   0.001   PHE D 369 
 TYR   0.013   0.001   TYR D  50 
 ARG   0.002   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    7)
  link_NAG-ASN         : angle       1.52602 (   21)
  hydrogen bonds       : bond        0.04748 (  321)
  hydrogen bonds       : angle       4.57415 (  984)
  SS BOND              : bond        0.00563 (    6)
  SS BOND              : angle       1.14541 (   12)
  covalent geometry    : bond        0.00366 ( 6745)
  covalent geometry    : angle       0.55864 ( 9166)

*********************** 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
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8335 (t0)
REVERT: A  465 GLU cc_start: 0.8651 (tt0) cc_final: 0.8323 (tt0)
REVERT: D   26 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8373 (mttm)
REVERT: D  115 ARG cc_start: 0.8731 (tpm-80) cc_final: 0.8035 (tpm170)
REVERT: D  182 GLU cc_start: 0.8722 (tt0) cc_final: 0.8374 (tt0)
REVERT: D  243 TYR cc_start: 0.9038 (t80) cc_final: 0.8817 (t80)
REVERT: D  270 MET cc_start: 0.8262 (tpt) cc_final: 0.8008 (tpp)
REVERT: D  287 GLN cc_start: 0.8668 (mp10) cc_final: 0.8188 (pm20)
REVERT: D  408 MET cc_start: 0.9262 (mmt) cc_final: 0.9012 (mmt)
REVERT: D  467 GLU cc_start: 0.8313 (mp0) cc_final: 0.7274 (mp0)
REVERT: D  470 LYS cc_start: 0.8744 (tppp) cc_final: 0.8539 (tppp)
REVERT: D  479 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: D  483 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: D  497 TYR cc_start: 0.8716 (m-80) cc_final: 0.8222 (m-80)
REVERT: D  531 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8283 (mt0)
REVERT: D  603 PHE cc_start: 0.8843 (t80) cc_final: 0.8425 (t80)
  outliers start: 23
  outliers final: 13
  residues processed: 120
  average time/residue: 1.1317
  time to fit residues: 143.2635
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  385 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   55 THR
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 75 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.099255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.076090 restraints weight = 12158.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.86
r_work: 0.2886 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6758  Z= 0.197
  Angle     :  0.583   7.303   9199  Z= 0.292
  Chirality :  0.043   0.159    976
  Planarity :  0.004   0.030   1179
  Dihedral  :  4.320  25.265   1012
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.30), residues: 792
  helix:  1.49 (0.26), residues: 410
  sheet:  1.87 (0.88), residues: 33
  loop :  0.25 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 239 
 PHE   0.015   0.001   PHE D 369 
 TYR   0.014   0.001   TYR D  41 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00202 (    7)
  link_NAG-ASN         : angle       1.54837 (   21)
  hydrogen bonds       : bond        0.04902 (  321)
  hydrogen bonds       : angle       4.60490 (  984)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.12415 (   12)
  covalent geometry    : bond        0.00450 ( 6745)
  covalent geometry    : angle       0.57837 ( 9166)

*********************** 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
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 GLU cc_start: 0.8680 (tt0) cc_final: 0.8361 (tt0)
REVERT: D   26 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8334 (mttm)
REVERT: D   86 GLN cc_start: 0.8575 (pp30) cc_final: 0.8335 (tm-30)
REVERT: D  114 LYS cc_start: 0.9456 (pptt) cc_final: 0.9242 (tmmt)
REVERT: D  115 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8081 (tpm170)
REVERT: D  182 GLU cc_start: 0.8759 (tt0) cc_final: 0.8419 (tt0)
REVERT: D  213 ASP cc_start: 0.9094 (t70) cc_final: 0.8737 (t0)
REVERT: D  243 TYR cc_start: 0.9045 (t80) cc_final: 0.8821 (t80)
REVERT: D  270 MET cc_start: 0.8309 (tpt) cc_final: 0.7989 (tpp)
REVERT: D  287 GLN cc_start: 0.8684 (mp10) cc_final: 0.8220 (pm20)
REVERT: D  467 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7200 (mp0)
REVERT: D  470 LYS cc_start: 0.8756 (tppp) cc_final: 0.8507 (tppp)
REVERT: D  479 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8351 (mt-10)
REVERT: D  483 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8355 (tm-30)
REVERT: D  497 TYR cc_start: 0.8707 (m-80) cc_final: 0.8262 (m-80)
REVERT: D  531 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (mt0)
REVERT: D  603 PHE cc_start: 0.8835 (t80) cc_final: 0.8403 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 112
  average time/residue: 1.1120
  time to fit residues: 131.4713
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  345 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 A residue  519 HIS
Chi-restraints excluded: chain D residue   55 THR
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  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  467 GLU
Chi-restraints excluded: chain D residue  531 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.099435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.076309 restraints weight = 12126.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.84
r_work: 0.2897 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6758  Z= 0.176
  Angle     :  0.583   7.849   9199  Z= 0.292
  Chirality :  0.042   0.155    976
  Planarity :  0.003   0.029   1179
  Dihedral  :  4.284  24.183   1012
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.17 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.30), residues: 792
  helix:  1.50 (0.26), residues: 409
  sheet:  1.60 (0.85), residues: 33
  loop :  0.28 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 239 
 PHE   0.015   0.001   PHE D 369 
 TYR   0.013   0.001   TYR D  41 
 ARG   0.003   0.000   ARG A 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00186 (    7)
  link_NAG-ASN         : angle       1.49938 (   21)
  hydrogen bonds       : bond        0.04772 (  321)
  hydrogen bonds       : angle       4.55812 (  984)
  SS BOND              : bond        0.00531 (    6)
  SS BOND              : angle       1.11361 (   12)
  covalent geometry    : bond        0.00404 ( 6745)
  covalent geometry    : angle       0.57834 ( 9166)

*********************** 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
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 GLU cc_start: 0.8700 (tt0) cc_final: 0.8388 (tt0)
REVERT: D   26 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8423 (mtmm)
REVERT: D   55 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7855 (p)
REVERT: D  115 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8111 (tpm170)
REVERT: D  213 ASP cc_start: 0.9070 (t70) cc_final: 0.8717 (t0)
REVERT: D  243 TYR cc_start: 0.9041 (t80) cc_final: 0.8819 (t80)
REVERT: D  270 MET cc_start: 0.8300 (tpt) cc_final: 0.7978 (tpp)
REVERT: D  287 GLN cc_start: 0.8667 (mp10) cc_final: 0.8217 (pm20)
REVERT: D  305 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8484 (tm-30)
REVERT: D  467 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7177 (mp0)
REVERT: D  470 LYS cc_start: 0.8757 (tppp) cc_final: 0.8500 (tppp)
REVERT: D  472 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8052 (mm-40)
REVERT: D  479 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8339 (mt-10)
REVERT: D  483 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: D  497 TYR cc_start: 0.8751 (m-80) cc_final: 0.8316 (m-80)
REVERT: D  531 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8286 (mt0)
REVERT: D  603 PHE cc_start: 0.8832 (t80) cc_final: 0.8418 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 112
  average time/residue: 1.1814
  time to fit residues: 139.3318
Evaluate side-chains
  113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  345 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 A residue  519 HIS
Chi-restraints excluded: chain D residue   55 THR
Chi-restraints excluded: chain D residue  115 ARG
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  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  467 GLU
Chi-restraints excluded: chain D residue  531 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0000
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 GLN ** 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 = 0.3421 r_free = 0.3421 target = 0.099970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.076899 restraints weight = 12181.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.85
r_work: 0.2906 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6758  Z= 0.155
  Angle     :  0.584   8.304   9199  Z= 0.290
  Chirality :  0.042   0.155    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.181  23.405   1012
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.60 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.30), residues: 792
  helix:  1.50 (0.26), residues: 409
  sheet:  0.62 (0.72), residues: 43
  loop :  0.39 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.002   0.000   ARG A 493 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    7)
  link_NAG-ASN         : angle       1.44473 (   21)
  hydrogen bonds       : bond        0.04640 (  321)
  hydrogen bonds       : angle       4.51398 (  984)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       1.03267 (   12)
  covalent geometry    : bond        0.00355 ( 6745)
  covalent geometry    : angle       0.57977 ( 9166)

*********************** 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
  120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7675 (ppp-140)
REVERT: A  465 GLU cc_start: 0.8716 (tt0) cc_final: 0.8419 (tt0)
REVERT: D   26 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8346 (mttm)
REVERT: D  115 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7990 (tpm170)
REVERT: D  213 ASP cc_start: 0.9071 (t70) cc_final: 0.8726 (t0)
REVERT: D  243 TYR cc_start: 0.9022 (t80) cc_final: 0.8787 (t80)
REVERT: D  270 MET cc_start: 0.8307 (tpt) cc_final: 0.7998 (tpp)
REVERT: D  287 GLN cc_start: 0.8659 (mp10) cc_final: 0.8223 (pm20)
REVERT: D  305 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8473 (tm-30)
REVERT: D  323 MET cc_start: 0.9192 (mmp) cc_final: 0.8967 (mmp)
REVERT: D  467 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7184 (mp0)
REVERT: D  470 LYS cc_start: 0.8747 (tppp) cc_final: 0.8470 (tppp)
REVERT: D  472 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8115 (mm-40)
REVERT: D  479 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8350 (mt-10)
REVERT: D  483 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8341 (tm-30)
REVERT: D  497 TYR cc_start: 0.8786 (m-80) cc_final: 0.8366 (m-80)
REVERT: D  518 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8288 (ttp80)
REVERT: D  531 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8297 (mt0)
REVERT: D  603 PHE cc_start: 0.8829 (t80) cc_final: 0.8423 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 111
  average time/residue: 1.3211
  time to fit residues: 154.0476
Evaluate side-chains
  113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  345 THR
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 D residue   55 THR
Chi-restraints excluded: chain D residue  115 ARG
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  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  467 GLU
Chi-restraints excluded: chain D residue  518 ARG
Chi-restraints excluded: chain D residue  531 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0370
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 GLN ** 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 = 0.3422 r_free = 0.3422 target = 0.099578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.076808 restraints weight = 12249.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.80
r_work: 0.2909 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6758  Z= 0.149
  Angle     :  0.596   8.665   9199  Z= 0.294
  Chirality :  0.042   0.152    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  4.151  22.965   1012
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.89 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.30), residues: 792
  helix:  1.63 (0.26), residues: 403
  sheet:  0.98 (0.83), residues: 38
  loop :  0.22 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.015   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.002   0.000   ARG A 493 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00199 (    7)
  link_NAG-ASN         : angle       1.44553 (   21)
  hydrogen bonds       : bond        0.04579 (  321)
  hydrogen bonds       : angle       4.49668 (  984)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       1.11471 (   12)
  covalent geometry    : bond        0.00341 ( 6745)
  covalent geometry    : angle       0.59124 ( 9166)

*********************** 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
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7738 (ppp-140)
REVERT: A  465 GLU cc_start: 0.8693 (tt0) cc_final: 0.8372 (tt0)
REVERT: D   26 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8236 (mttm)
REVERT: D  115 ARG cc_start: 0.8734 (tpm-80) cc_final: 0.8076 (tpm170)
REVERT: D  213 ASP cc_start: 0.9086 (t70) cc_final: 0.8746 (t0)
REVERT: D  243 TYR cc_start: 0.8916 (t80) cc_final: 0.8675 (t80)
REVERT: D  270 MET cc_start: 0.8247 (tpt) cc_final: 0.7920 (tpp)
REVERT: D  287 GLN cc_start: 0.8694 (mp10) cc_final: 0.8279 (pm20)
REVERT: D  305 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8426 (tm-30)
REVERT: D  467 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7095 (mp0)
REVERT: D  470 LYS cc_start: 0.8729 (tppp) cc_final: 0.8433 (tppp)
REVERT: D  483 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: D  497 TYR cc_start: 0.8770 (m-80) cc_final: 0.8379 (m-80)
REVERT: D  603 PHE cc_start: 0.8769 (t80) cc_final: 0.8343 (t80)
  outliers start: 21
  outliers final: 12
  residues processed: 114
  average time/residue: 1.1610
  time to fit residues: 139.4001
Evaluate side-chains
  111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 ARG
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   55 THR
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  305 GLN
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  467 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0470
   chunk 66 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 36 optimal weight:    0.1980
   overall best weight:    0.3078

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN
D 340 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.101479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.078681 restraints weight = 12321.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.82
r_work: 0.2941 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6758  Z= 0.122
  Angle     :  0.583   8.992   9199  Z= 0.289
  Chirality :  0.041   0.155    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  3.987  23.556   1012
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.03 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.30), residues: 792
  helix:  1.54 (0.26), residues: 413
  sheet:  0.53 (0.72), residues: 43
  loop :  0.17 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 165 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.014   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.003   0.000   ARG D 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    7)
  link_NAG-ASN         : angle       1.37987 (   21)
  hydrogen bonds       : bond        0.04270 (  321)
  hydrogen bonds       : angle       4.45743 (  984)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.02262 (   12)
  covalent geometry    : bond        0.00273 ( 6745)
  covalent geometry    : angle       0.57917 ( 9166)

********************** 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
  115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7766 (ppp-140)
REVERT: A  357 ARG cc_start: 0.8692 (ptm160) cc_final: 0.8123 (ttt90)
REVERT: A  465 GLU cc_start: 0.8687 (tt0) cc_final: 0.8340 (tt0)
REVERT: D   26 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8228 (mttp)
REVERT: D  115 ARG cc_start: 0.8695 (tpm-80) cc_final: 0.8093 (tpm170)
REVERT: D  213 ASP cc_start: 0.9065 (t70) cc_final: 0.8725 (t0)
REVERT: D  243 TYR cc_start: 0.8861 (t80) cc_final: 0.8618 (t80)
REVERT: D  270 MET cc_start: 0.8121 (tpt) cc_final: 0.7860 (tpp)
REVERT: D  287 GLN cc_start: 0.8690 (mp10) cc_final: 0.8274 (pm20)
REVERT: D  340 GLN cc_start: 0.7952 (tt0) cc_final: 0.7669 (tm-30)
REVERT: D  467 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7107 (mp0)
REVERT: D  470 LYS cc_start: 0.8745 (tppp) cc_final: 0.8448 (tppp)
REVERT: D  479 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8237 (mt-10)
REVERT: D  483 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: D  497 TYR cc_start: 0.8795 (m-80) cc_final: 0.8405 (m-80)
REVERT: D  603 PHE cc_start: 0.8771 (t80) cc_final: 0.8325 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 112
  average time/residue: 1.2325
  time to fit residues: 145.4678
Evaluate side-chains
  110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   55 THR
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  467 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 31 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   chunk 10 optimal weight:    0.4980
   chunk 77 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.101112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.078127 restraints weight = 12224.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.84
r_work: 0.2943 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6758  Z= 0.132
  Angle     :  0.601  11.539   9199  Z= 0.298
  Chirality :  0.042   0.156    976
  Planarity :  0.003   0.028   1179
  Dihedral  :  3.973  24.554   1012
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.17 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.30), residues: 792
  helix:  1.54 (0.26), residues: 413
  sheet:  0.55 (0.72), residues: 43
  loop :  0.21 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 374 
 PHE   0.015   0.001   PHE D 369 
 TYR   0.012   0.001   TYR D  41 
 ARG   0.005   0.000   ARG D 518 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    7)
  link_NAG-ASN         : angle       1.38106 (   21)
  hydrogen bonds       : bond        0.04323 (  321)
  hydrogen bonds       : angle       4.46098 (  984)
  SS BOND              : bond        0.00445 (    6)
  SS BOND              : angle       1.03393 (   12)
  covalent geometry    : bond        0.00298 ( 6745)
  covalent geometry    : angle       0.59755 ( 9166)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5222.34 seconds
wall clock time: 90 minutes 9.31 seconds (5409.31 seconds total)