Starting phenix.real_space_refine
on Mon Jul 28 17:34:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xn3_38496/07_2025/8xn3_38496.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4872 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4161      2.51       5
     N    1076      2.21       5
     O    1230      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 6505
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4987
    Chain: "B"
      Number of atoms: 1548
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1548
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 85
          Unusual residues: {' ZN': 1, 'NAG': 6}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A  34 " occ=0.63
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  34 " occ=0.37
  Time building chain proxies: 9.51, per 1000 atoms: 1.46
  Number of scatterers: 6505
  At special positions: 0
  Unit cell: (97.768, 69.488, 121.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1230      8.00
     N    1076      7.00
     C    4161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 103 "
      " NAG A 704 " - " ASN A 432 "
      " NAG A 705 " - " ASN A 546 "
      " NAG A 706 " - " ASN A 322 "
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 707 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 707 " - pdb=" NE2 HIS A 374 "


  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      54.6% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.668A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A  38 " --> pdb=" O  AHIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.535A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 102
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.182A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.779A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 3.511A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.703A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.137A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 509
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.429A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.842A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 342
      removed outlier: 3.532A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.698A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134
      removed outlier: 3.573A  pdb=" N   ASN A 134 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLU A 140 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.508A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.164A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.864A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    320 hydrogen bonds defined for protein.
    931 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: 1.72

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1084
        1.32 -     1.44: 1943
        1.44 -     1.57: 3605
        1.57 -     1.69: 0
        1.69 -     1.82: 58
  Bond restraints: 6690
  Sorted by residual:
  bond pdb=" C   PRO B 491 "
       pdb=" O   PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.238  1.195  0.043 1.22e-02 6.72e+03 1.25e+01
  bond pdb=" CA  SER B 490 "
       pdb=" CB  SER B 490 "
    ideal  model  delta    sigma   weight residual
    1.532  1.487  0.045 1.50e-02 4.44e+03 9.09e+00
  bond pdb=" N   PRO B 491 "
       pdb=" CA  PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.470  1.430  0.040 1.34e-02 5.57e+03 8.86e+00
  bond pdb=" N   CYS B 488 "
       pdb=" CA  CYS B 488 "
    ideal  model  delta    sigma   weight residual
    1.464  1.493 -0.029 1.25e-02 6.40e+03 5.51e+00
  bond pdb=" N   GLN A  42 "
       pdb=" CA  GLN A  42 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.30e-02 5.92e+03 4.65e+00
  ... (remaining 6685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 8922
        1.82 -     3.65: 151
        3.65 -     5.47: 19
        5.47 -     7.29: 4
        7.29 -     9.11: 1
  Bond angle restraints: 9097
  Sorted by residual:
  angle pdb=" N   TYR B 489 "
        pdb=" CA  TYR B 489 "
        pdb=" CB  TYR B 489 "
      ideal   model   delta    sigma   weight residual
     110.87  101.76    9.11 1.51e+00 4.39e-01 3.64e+01
  angle pdb=" C   ASN A 338 "
        pdb=" CA  ASN A 338 "
        pdb=" CB  ASN A 338 "
      ideal   model   delta    sigma   weight residual
     117.23  110.19    7.04 1.36e+00 5.41e-01 2.68e+01
  angle pdb=" CA  ASN A 338 "
        pdb=" C   ASN A 338 "
        pdb=" N   VAL A 339 "
      ideal   model   delta    sigma   weight residual
     119.98  116.73    3.25 8.50e-01 1.38e+00 1.46e+01
  angle pdb=" C   SER B 494 "
        pdb=" CA  SER B 494 "
        pdb=" CB  SER B 494 "
      ideal   model   delta    sigma   weight residual
     109.51  115.06   -5.55 1.71e+00 3.42e-01 1.06e+01
  angle pdb=" CA  SER B 490 "
        pdb=" C   SER B 490 "
        pdb=" O   SER B 490 "
      ideal   model   delta    sigma   weight residual
     120.63  117.31    3.32 1.03e+00 9.43e-01 1.04e+01
  ... (remaining 9092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 3651
       17.25 -    34.49: 309
       34.49 -    51.74: 42
       51.74 -    68.98: 20
       68.98 -    86.23: 8
  Dihedral angle restraints: 4030
    sinusoidal: 1702
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.98   53.98     1      1.00e+01 1.00e-02 3.95e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.63  -52.63     1      1.00e+01 1.00e-02 3.77e+01
  dihedral pdb=" CA  SER B 494 "
           pdb=" C   SER B 494 "
           pdb=" N   TYR B 495 "
           pdb=" CA  TYR B 495 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.96   19.04     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 4027 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 867
       0.065 -    0.130: 96
       0.130 -    0.195: 2
       0.195 -    0.260: 1
       0.260 -    0.325: 2
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" C1  NAG A 706 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 706 "
            pdb=" O5  NAG A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" C1  NAG A 704 "
            pdb=" ND2 ASN A 432 "
            pdb=" C2  NAG A 704 "
            pdb=" O5  NAG A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  GLN B 493 "
            pdb=" N   GLN B 493 "
            pdb=" C   GLN B 493 "
            pdb=" CB  GLN B 493 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 965 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 498 "   -0.200 9.50e-02 1.11e+02   8.97e-02 4.94e+00
        pdb=" NE  ARG B 498 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 498 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 498 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 498 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.76e+00
        pdb=" N   PRO A 583 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  19 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   SER A  19 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   SER A  19 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR A  20 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 71
        2.63 -     3.20: 5885
        3.20 -     3.77: 10302
        3.77 -     4.33: 14250
        4.33 -     4.90: 23075
  Nonbonded interactions: 53583
  Sorted by model distance:
  nonbonded pdb=" CD  GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.067 2.460
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.095 2.230
  nonbonded pdb=" OE1 GLU A 402 "
            pdb="ZN    ZN A 707 "
     model   vdw
     2.096 2.230
  nonbonded pdb=" ND2 ASN B 417 "
            pdb=" CD1 LEU B 455 "
     model   vdw
     2.211 3.540
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.263 3.040
  ... (remaining 53578 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=0.37 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:             104.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     26.210
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:14.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  145.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6027
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      :  0.005   0.209   6705  Z= 0.220
  Angle     :  0.598   9.615   9129  Z= 0.333
  Chirality :  0.044   0.325    968
  Planarity :  0.005   0.090   1172
  Dihedral  : 13.619  86.227   2515
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  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:  1.25 (0.31), residues: 790
  helix:  1.74 (0.26), residues: 401
  sheet:  1.03 (0.74), residues: 48
  loop : -0.27 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 566 
 HIS   0.013   0.002   HIS A 378 
 PHE   0.019   0.001   PHE A 400 
 TYR   0.020   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00820 (    6)
  link_NAG-ASN         : angle       3.74215 (   18)
  hydrogen bonds       : bond        0.10828 (  320)
  hydrogen bonds       : angle       5.04774 (  931)
  metal coordination   : bond        0.20674 (    2)
  SS BOND              : bond        0.00618 (    7)
  SS BOND              : angle       0.57254 (   14)
  covalent geometry    : bond        0.00331 ( 6690)
  covalent geometry    : angle       0.57458 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 TYR cc_start: 0.6241 (t80) cc_final: 0.5817 (t80)
REVERT: A   61 ASN cc_start: 0.5958 (m110) cc_final: 0.5753 (m-40)
REVERT: A   62 MET cc_start: 0.7491 (ttt) cc_final: 0.7180 (ttp)
REVERT: A   64 ASN cc_start: 0.7660 (m-40) cc_final: 0.7332 (m110)
REVERT: A   67 ASP cc_start: 0.7027 (m-30) cc_final: 0.6692 (m-30)
REVERT: A   69 TRP cc_start: 0.7966 (t-100) cc_final: 0.7742 (t-100)
REVERT: A   87 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6175 (mm-30)
REVERT: A  160 GLU cc_start: 0.6808 (tt0) cc_final: 0.6366 (tm-30)
REVERT: A  187 LYS cc_start: 0.6525 (mmmt) cc_final: 0.6072 (mmtp)
REVERT: A  192 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7124 (mpp-170)
REVERT: A  202 TYR cc_start: 0.7627 (t80) cc_final: 0.7306 (t80)
REVERT: A  206 ASP cc_start: 0.7938 (t0) cc_final: 0.7541 (t0)
REVERT: A  245 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6605 (ttp-170)
REVERT: A  285 PHE cc_start: 0.6300 (m-80) cc_final: 0.6017 (m-10)
REVERT: A  351 LEU cc_start: 0.8224 (mt) cc_final: 0.7764 (mp)
REVERT: A  397 ASN cc_start: 0.7184 (p0) cc_final: 0.6917 (p0)
REVERT: A  398 GLU cc_start: 0.7227 (pt0) cc_final: 0.6768 (pt0)
REVERT: A  432 ASN cc_start: 0.5817 (m-40) cc_final: 0.5423 (p0)
REVERT: A  455 MET cc_start: 0.7353 (tpt) cc_final: 0.7108 (tpp)
REVERT: A  465 LYS cc_start: 0.7405 (mttp) cc_final: 0.7092 (mttp)
REVERT: A  482 ARG cc_start: 0.6649 (ttm170) cc_final: 0.6444 (mtt180)
REVERT: A  483 GLU cc_start: 0.6695 (tp30) cc_final: 0.6373 (tp30)
REVERT: A  488 VAL cc_start: 0.7340 (p) cc_final: 0.6557 (t)
REVERT: A  489 GLU cc_start: 0.6545 (pm20) cc_final: 0.5507 (pm20)
REVERT: A  518 ARG cc_start: 0.6949 (ttp80) cc_final: 0.6309 (ttp80)
REVERT: A  544 ILE cc_start: 0.7596 (pt) cc_final: 0.7343 (pp)
REVERT: A  564 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6766 (mm-30)
REVERT: A  594 TRP cc_start: 0.6045 (t60) cc_final: 0.5779 (t-100)
REVERT: A  602 SER cc_start: 0.6763 (m) cc_final: 0.6122 (p)
REVERT: A  610 TRP cc_start: 0.7239 (t60) cc_final: 0.6911 (t60)
REVERT: A  613 TYR cc_start: 0.6606 (p90) cc_final: 0.6261 (p90)
REVERT: B  396 TYR cc_start: 0.6643 (m-80) cc_final: 0.6016 (m-80)
REVERT: B  409 GLN cc_start: 0.7880 (mt0) cc_final: 0.7504 (mt0)
REVERT: B  453 TYR cc_start: 0.8016 (p90) cc_final: 0.7712 (p90)
REVERT: B  462 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7527 (mmtp)
REVERT: B  509 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7263 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 1.0087
  time to fit residues: 240.7426
Evaluate side-chains
  200 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 59 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0270
   chunk 37 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0970
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.2636

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

Flipped N/Q/H residues before XYZ refinement:
** A  34 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 340 GLN
A 345 HIS
A 442 GLN
A 535 HIS
A 601 ASN
B 354 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 505 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.176564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.161900 restraints weight = 22225.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 4.19
r_work: 0.4066 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6705  Z= 0.161
  Angle     :  0.613   9.635   9129  Z= 0.310
  Chirality :  0.049   0.366    968
  Planarity :  0.005   0.042   1172
  Dihedral  :  5.766  52.201    987
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.38 %
    Favored  : 84.46 %
  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:  1.05 (0.30), residues: 790
  helix:  1.61 (0.26), residues: 401
  sheet:  1.43 (0.80), residues: 48
  loop : -0.49 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 302 
 HIS   0.007   0.002   HIS A 540 
 PHE   0.028   0.002   PHE A 369 
 TYR   0.016   0.001   TYR A 385 
 ARG   0.003   0.001   ARG A 393 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00950 (    6)
  link_NAG-ASN         : angle       4.23202 (   18)
  hydrogen bonds       : bond        0.05011 (  320)
  hydrogen bonds       : angle       4.65449 (  931)
  metal coordination   : bond        0.00531 (    2)
  SS BOND              : bond        0.00299 (    7)
  SS BOND              : angle       0.90310 (   14)
  covalent geometry    : bond        0.00345 ( 6690)
  covalent geometry    : angle       0.58364 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 200
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6411 (mm)
REVERT: A   63 ASN cc_start: 0.7619 (m-40) cc_final: 0.7081 (m-40)
REVERT: A   98 GLN cc_start: 0.8205 (mm110) cc_final: 0.7961 (mm-40)
REVERT: A  190 MET cc_start: 0.7668 (tmm) cc_final: 0.7421 (tmm)
REVERT: A  201 ASP cc_start: 0.7657 (t70) cc_final: 0.7357 (m-30)
REVERT: A  202 TYR cc_start: 0.8224 (t80) cc_final: 0.7917 (t80)
REVERT: A  483 GLU cc_start: 0.7520 (tp30) cc_final: 0.7276 (tp30)
REVERT: A  514 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7623 (mtm-85)
REVERT: A  518 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7073 (ttp80)
REVERT: B  494 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8233 (t)
  outliers start: 15
  outliers final: 6
  residues processed: 205
  average time/residue: 1.4470
  time to fit residues: 312.6566
Evaluate side-chains
  208 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 199
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  494 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0980
   chunk 16 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 54 optimal weight:    0.2980
   chunk 73 optimal weight:    0.4980
   chunk 60 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0870
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.2158

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 ASN
A  81 GLN
A 345 HIS
B 409 GLN
B 414 GLN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.179258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.164016 restraints weight = 23988.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 4.41
r_work: 0.4051 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4049 r_free = 0.4049    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6705  Z= 0.151
  Angle     :  0.615   9.653   9129  Z= 0.313
  Chirality :  0.049   0.383    968
  Planarity :  0.005   0.049   1172
  Dihedral  :  5.636  50.691    987
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.40 %
    Favored  : 80.58 %
  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:  1.02 (0.30), residues: 790
  helix:  1.69 (0.25), residues: 401
  sheet:  1.32 (0.77), residues: 48
  loop : -0.65 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 610 
 HIS   0.007   0.002   HIS A 417 
 PHE   0.026   0.002   PHE A 369 
 TYR   0.019   0.002   TYR A  50 
 ARG   0.008   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01421 (    6)
  link_NAG-ASN         : angle       4.38011 (   18)
  hydrogen bonds       : bond        0.04835 (  320)
  hydrogen bonds       : angle       4.75080 (  931)
  metal coordination   : bond        0.00085 (    2)
  SS BOND              : bond        0.00264 (    7)
  SS BOND              : angle       0.81050 (   14)
  covalent geometry    : bond        0.00325 ( 6690)
  covalent geometry    : angle       0.58318 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 190
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7784 (ttmm) cc_final: 0.7553 (ttmm)
REVERT: A  190 MET cc_start: 0.7713 (tmm) cc_final: 0.7448 (tmm)
REVERT: A  202 TYR cc_start: 0.8266 (t80) cc_final: 0.7961 (t80)
REVERT: A  482 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7268 (mmt90)
REVERT: A  489 GLU cc_start: 0.6952 (pm20) cc_final: 0.6749 (pm20)
REVERT: A  514 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (mtm-85)
REVERT: A  518 ARG cc_start: 0.7318 (ttp80) cc_final: 0.6989 (ttp80)
REVERT: B  494 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8297 (t)
REVERT: B  509 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8140 (mtt90)
  outliers start: 21
  outliers final: 7
  residues processed: 194
  average time/residue: 1.1512
  time to fit residues: 235.1277
Evaluate side-chains
  185 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 176
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  494 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0770
   chunk 49 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 36 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.2694

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  96 GLN
A 345 HIS
B 360 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 506 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.175082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.162635 restraints weight = 14637.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.4225 rms_B_bonded: 3.02
r_work: 0.4107 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4103
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4103 r_free = 0.4103    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4103 r_free = 0.4103    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4103
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6705  Z= 0.171
  Angle     :  0.658   9.866   9129  Z= 0.335
  Chirality :  0.050   0.415    968
  Planarity :  0.005   0.043   1172
  Dihedral  :  5.529  46.018    987
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.00 %
    Favored  : 77.27 %
  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:  0.74 (0.29), residues: 790
  helix:  1.43 (0.25), residues: 401
  sheet:  1.17 (0.76), residues: 49
  loop : -0.75 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 610 
 HIS   0.008   0.001   HIS A 417 
 PHE   0.025   0.002   PHE A 369 
 TYR   0.025   0.002   TYR B 380 
 ARG   0.006   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01026 (    6)
  link_NAG-ASN         : angle       4.34548 (   18)
  hydrogen bonds       : bond        0.04922 (  320)
  hydrogen bonds       : angle       4.85212 (  931)
  metal coordination   : bond        0.00067 (    2)
  SS BOND              : bond        0.00259 (    7)
  SS BOND              : angle       0.93842 (   14)
  covalent geometry    : bond        0.00372 ( 6690)
  covalent geometry    : angle       0.62954 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6761 (mp) cc_final: 0.6288 (mt)
REVERT: A   98 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7849 (mm-40)
REVERT: A  103 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.6352 (t160)
REVERT: A  201 ASP cc_start: 0.7905 (m-30) cc_final: 0.7145 (m-30)
REVERT: A  202 TYR cc_start: 0.8202 (t80) cc_final: 0.7852 (t80)
REVERT: A  455 MET cc_start: 0.7745 (tpt) cc_final: 0.6899 (tpt)
REVERT: A  480 MET cc_start: 0.6122 (ttm) cc_final: 0.5912 (ttm)
REVERT: A  514 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7785 (mtm180)
REVERT: A  518 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6764 (ttp80)
  outliers start: 19
  outliers final: 8
  residues processed: 199
  average time/residue: 1.2586
  time to fit residues: 264.1852
Evaluate side-chains
  195 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 59 optimal weight:    0.0470
   chunk 71 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.3014

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 137 ASN
A 345 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 437 ASN
B 439 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.173525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.158844 restraints weight = 21470.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 4.10
r_work: 0.4032 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4032 r_free = 0.4032    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4032 r_free = 0.4032    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6705  Z= 0.182
  Angle     :  0.684  10.150   9129  Z= 0.346
  Chirality :  0.050   0.433    968
  Planarity :  0.005   0.050   1172
  Dihedral  :  5.447  42.916    987
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 21.73 %
    Favored  : 74.68 %
  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:  0.62 (0.29), residues: 790
  helix:  1.37 (0.25), residues: 401
  sheet:  1.22 (0.76), residues: 49
  loop : -0.86 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 610 
 HIS   0.008   0.002   HIS A 417 
 PHE   0.024   0.002   PHE A 369 
 TYR   0.023   0.002   TYR B 380 
 ARG   0.011   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01166 (    6)
  link_NAG-ASN         : angle       4.37177 (   18)
  hydrogen bonds       : bond        0.05018 (  320)
  hydrogen bonds       : angle       4.91022 (  931)
  metal coordination   : bond        0.00066 (    2)
  SS BOND              : bond        0.00316 (    7)
  SS BOND              : angle       0.93287 (   14)
  covalent geometry    : bond        0.00402 ( 6690)
  covalent geometry    : angle       0.65569 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6531 (mt)
REVERT: A   98 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7926 (mm-40)
REVERT: A  103 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6290 (t160)
REVERT: A  131 LYS cc_start: 0.8422 (ptmm) cc_final: 0.7648 (ttmm)
REVERT: A  190 MET cc_start: 0.7680 (tmm) cc_final: 0.7455 (tmm)
REVERT: A  201 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7208 (m-30)
REVERT: A  202 TYR cc_start: 0.8263 (t80) cc_final: 0.7838 (t80)
REVERT: A  314 PHE cc_start: 0.7996 (t80) cc_final: 0.7664 (t80)
REVERT: A  455 MET cc_start: 0.7858 (tpt) cc_final: 0.7076 (tpt)
REVERT: A  480 MET cc_start: 0.6257 (ttm) cc_final: 0.6044 (ttm)
REVERT: A  483 GLU cc_start: 0.7427 (tp30) cc_final: 0.7129 (mp0)
REVERT: A  518 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6922 (ttp80)
REVERT: B  498 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (mtt90)
  outliers start: 25
  outliers final: 13
  residues processed: 203
  average time/residue: 1.1067
  time to fit residues: 236.7875
Evaluate side-chains
  201 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  437 ASN
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   chunk 70 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 59 optimal weight:    0.0010
   chunk 18 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A 239 HIS
A 345 HIS
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
B 450 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.172043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.156445 restraints weight = 25380.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 4.60
r_work: 0.3980 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6705  Z= 0.221
  Angle     :  0.720  10.552   9129  Z= 0.369
  Chirality :  0.052   0.413    968
  Planarity :  0.006   0.061   1172
  Dihedral  :  5.488  42.563    987
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.87 %
    Favored  : 74.24 %
  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:  0.41 (0.29), residues: 790
  helix:  1.22 (0.25), residues: 400
  sheet:  1.11 (0.76), residues: 48
  loop : -1.00 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 610 
 HIS   0.009   0.002   HIS A 417 
 PHE   0.033   0.002   PHE A 369 
 TYR   0.025   0.002   TYR B 380 
 ARG   0.014   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01129 (    6)
  link_NAG-ASN         : angle       4.42007 (   18)
  hydrogen bonds       : bond        0.05388 (  320)
  hydrogen bonds       : angle       5.00371 (  931)
  metal coordination   : bond        0.00050 (    2)
  SS BOND              : bond        0.00673 (    7)
  SS BOND              : angle       1.24977 (   14)
  covalent geometry    : bond        0.00484 ( 6690)
  covalent geometry    : angle       0.69230 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 194
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6620 (mp)
REVERT: A   98 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7960 (mm-40)
REVERT: A  103 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6370 (t0)
REVERT: A  131 LYS cc_start: 0.8441 (ptmm) cc_final: 0.7827 (ttmm)
REVERT: A  190 MET cc_start: 0.7760 (tmm) cc_final: 0.7535 (tmm)
REVERT: A  201 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7358 (m-30)
REVERT: A  202 TYR cc_start: 0.8313 (t80) cc_final: 0.7875 (t80)
REVERT: A  455 MET cc_start: 0.7945 (tpt) cc_final: 0.6998 (tpt)
REVERT: A  480 MET cc_start: 0.6447 (ttm) cc_final: 0.6110 (ttm)
REVERT: A  483 GLU cc_start: 0.7462 (tp30) cc_final: 0.7168 (mp0)
REVERT: A  518 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7071 (ttp80)
REVERT: A  582 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6805 (mmm160)
REVERT: B  396 TYR cc_start: 0.7181 (m-80) cc_final: 0.6739 (m-80)
REVERT: B  454 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8036 (ttm-80)
REVERT: B  498 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8281 (mtt90)
  outliers start: 27
  outliers final: 11
  residues processed: 206
  average time/residue: 1.6499
  time to fit residues: 359.2287
Evaluate side-chains
  203 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 188
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  494 SER
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 30 optimal weight:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 345 HIS
B 417 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.174445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.161049 restraints weight = 15726.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.4167 rms_B_bonded: 3.44
r_work: 0.4040 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4042 r_free = 0.4042    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4042 r_free = 0.4042    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6705  Z= 0.243
  Angle     :  0.752  11.062   9129  Z= 0.386
  Chirality :  0.053   0.412    968
  Planarity :  0.006   0.051   1172
  Dihedral  :  5.572  41.245    987
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.60 %
    Favored  : 72.95 %
  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:  0.24 (0.29), residues: 790
  helix:  1.14 (0.25), residues: 396
  sheet:  0.76 (0.72), residues: 51
  loop : -1.10 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 610 
 HIS   0.007   0.002   HIS A 417 
 PHE   0.033   0.002   PHE A 369 
 TYR   0.023   0.002   TYR A  50 
 ARG   0.011   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01121 (    6)
  link_NAG-ASN         : angle       4.53141 (   18)
  hydrogen bonds       : bond        0.05636 (  320)
  hydrogen bonds       : angle       5.13781 (  931)
  metal coordination   : bond        0.00100 (    2)
  SS BOND              : bond        0.00439 (    7)
  SS BOND              : angle       1.59153 (   14)
  covalent geometry    : bond        0.00536 ( 6690)
  covalent geometry    : angle       0.72269 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7839 (mm-40)
REVERT: A  103 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6071 (t0)
REVERT: A  131 LYS cc_start: 0.8431 (ptmm) cc_final: 0.7777 (ttmm)
REVERT: A  192 ARG cc_start: 0.7809 (mpp80) cc_final: 0.7602 (mpp-170)
REVERT: A  201 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7420 (m-30)
REVERT: A  202 TYR cc_start: 0.8267 (t80) cc_final: 0.7840 (t80)
REVERT: A  455 MET cc_start: 0.7820 (tpt) cc_final: 0.6830 (tpt)
REVERT: A  476 LYS cc_start: 0.7486 (tptm) cc_final: 0.7188 (tppp)
REVERT: A  480 MET cc_start: 0.6343 (ttm) cc_final: 0.6021 (ttm)
REVERT: A  483 GLU cc_start: 0.7228 (tp30) cc_final: 0.6945 (mp0)
REVERT: A  518 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6954 (ttp80)
REVERT: B  396 TYR cc_start: 0.7222 (m-80) cc_final: 0.6891 (m-80)
REVERT: B  430 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7802 (t)
REVERT: B  498 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8229 (mtt90)
  outliers start: 24
  outliers final: 11
  residues processed: 204
  average time/residue: 1.4328
  time to fit residues: 308.4070
Evaluate side-chains
  198 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 183
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  103 ASN
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0980
   chunk 56 optimal weight:    0.3980
   chunk 45 optimal weight:    0.1980
   chunk 21 optimal weight:    0.0770
   chunk 50 optimal weight:    0.1980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.1938

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 345 HIS
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.177521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.165180 restraints weight = 14174.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 3.03
r_work: 0.4100 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4100
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4100 r_free = 0.4100    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4100 r_free = 0.4100    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4100
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6705  Z= 0.154
  Angle     :  0.704  10.304   9129  Z= 0.355
  Chirality :  0.049   0.379    968
  Planarity :  0.005   0.068   1172
  Dihedral  :  5.222  41.124    987
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.46 %
    Favored  : 71.94 %
  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:  0.41 (0.30), residues: 790
  helix:  1.25 (0.26), residues: 405
  sheet:  0.90 (0.76), residues: 50
  loop : -1.06 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 610 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.033   0.002   PHE A 369 
 TYR   0.020   0.002   TYR A  50 
 ARG   0.015   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01154 (    6)
  link_NAG-ASN         : angle       4.25540 (   18)
  hydrogen bonds       : bond        0.04870 (  320)
  hydrogen bonds       : angle       5.06198 (  931)
  metal coordination   : bond        0.00047 (    2)
  SS BOND              : bond        0.00207 (    7)
  SS BOND              : angle       1.13881 (   14)
  covalent geometry    : bond        0.00337 ( 6690)
  covalent geometry    : angle       0.67747 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7773 (mm-40)
REVERT: A  131 LYS cc_start: 0.8367 (ptmm) cc_final: 0.7798 (ttmm)
REVERT: A  190 MET cc_start: 0.7673 (tmm) cc_final: 0.7397 (tmm)
REVERT: A  201 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7358 (m-30)
REVERT: A  202 TYR cc_start: 0.8247 (t80) cc_final: 0.7835 (t80)
REVERT: A  248 LEU cc_start: 0.8319 (mt) cc_final: 0.8077 (mm)
REVERT: A  310 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6607 (mt-10)
REVERT: A  455 MET cc_start: 0.7782 (tpt) cc_final: 0.6727 (tpt)
REVERT: A  476 LYS cc_start: 0.7441 (tptm) cc_final: 0.7171 (tppp)
REVERT: A  480 MET cc_start: 0.6344 (ttm) cc_final: 0.5921 (ttm)
REVERT: A  483 GLU cc_start: 0.7149 (tp30) cc_final: 0.6923 (mp0)
REVERT: A  509 ASP cc_start: 0.6763 (t0) cc_final: 0.6434 (t70)
REVERT: A  518 ARG cc_start: 0.7082 (ttp80) cc_final: 0.6808 (ttp80)
REVERT: A  536 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6648 (mt-10)
REVERT: B  396 TYR cc_start: 0.7121 (m-80) cc_final: 0.6685 (m-80)
REVERT: B  430 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7792 (t)
REVERT: B  454 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8043 (ttm-80)
REVERT: B  498 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8233 (mtt90)
  outliers start: 25
  outliers final: 12
  residues processed: 205
  average time/residue: 1.1660
  time to fit residues: 252.1865
Evaluate side-chains
  203 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 186
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  454 ARG
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 71 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 52 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0980
   chunk 50 optimal weight:    0.0970
   overall best weight:    0.1576

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 345 HIS
A 556 ASN
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 439 ASN
B 448 ASN
B 450 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.177902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.162451 restraints weight = 25955.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4194 rms_B_bonded: 4.64
r_work: 0.4027 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4026 r_free = 0.4026    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4026 r_free = 0.4026    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   6705  Z= 0.153
  Angle     :  0.721  10.771   9129  Z= 0.362
  Chirality :  0.049   0.364    968
  Planarity :  0.005   0.043   1172
  Dihedral  :  5.270  40.479    987
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 25.76 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.30), residues: 790
  helix:  1.29 (0.26), residues: 405
  sheet:  1.07 (0.75), residues: 51
  loop : -1.04 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 610 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.034   0.002   PHE A 369 
 TYR   0.030   0.002   TYR B 380 
 ARG   0.003   0.001   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00974 (    6)
  link_NAG-ASN         : angle       4.05196 (   18)
  hydrogen bonds       : bond        0.04737 (  320)
  hydrogen bonds       : angle       5.14033 (  931)
  metal coordination   : bond        0.00062 (    2)
  SS BOND              : bond        0.00521 (    7)
  SS BOND              : angle       2.19714 (   14)
  covalent geometry    : bond        0.00341 ( 6690)
  covalent geometry    : angle       0.69369 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.7020 (mp10) cc_final: 0.6810 (mp10)
REVERT: A  131 LYS cc_start: 0.8362 (ptmm) cc_final: 0.7775 (ttmm)
REVERT: A  152 MET cc_start: 0.7574 (mmm) cc_final: 0.7359 (tpp)
REVERT: A  190 MET cc_start: 0.7755 (tmm) cc_final: 0.7453 (tmm)
REVERT: A  201 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7664 (m-30)
REVERT: A  202 TYR cc_start: 0.8330 (t80) cc_final: 0.7921 (t80)
REVERT: A  248 LEU cc_start: 0.8362 (mt) cc_final: 0.8153 (mm)
REVERT: A  310 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6758 (mt-10)
REVERT: A  455 MET cc_start: 0.7769 (tpt) cc_final: 0.6759 (tpt)
REVERT: A  476 LYS cc_start: 0.7621 (tptm) cc_final: 0.7274 (tppp)
REVERT: A  480 MET cc_start: 0.6673 (ttm) cc_final: 0.6195 (ttm)
REVERT: A  483 GLU cc_start: 0.7503 (tp30) cc_final: 0.7210 (mp0)
REVERT: A  509 ASP cc_start: 0.6868 (t70) cc_final: 0.6528 (t70)
REVERT: A  518 ARG cc_start: 0.7266 (ttp80) cc_final: 0.6964 (ttp80)
REVERT: A  536 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6708 (mt-10)
REVERT: B  396 TYR cc_start: 0.7194 (m-80) cc_final: 0.6715 (m-80)
REVERT: B  430 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7943 (t)
REVERT: B  454 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8088 (ttm-80)
REVERT: B  495 TYR cc_start: 0.7477 (m-80) cc_final: 0.7002 (m-10)
REVERT: B  498 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8238 (mtt90)
  outliers start: 23
  outliers final: 13
  residues processed: 206
  average time/residue: 1.1345
  time to fit residues: 247.1949
Evaluate side-chains
  211 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  454 ARG
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 52 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0980
   chunk 6 optimal weight:    0.0010
   chunk 54 optimal weight:    0.2980
   chunk 58 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0970
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.0702

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A  96 GLN
A 442 GLN
B 448 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.177442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.164875 restraints weight = 15914.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 3.17
r_work: 0.4132 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4131 r_free = 0.4131    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4131 r_free = 0.4131    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6855
moved from start:          0.4549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6705  Z= 0.142
  Angle     :  0.710  10.640   9129  Z= 0.355
  Chirality :  0.047   0.347    968
  Planarity :  0.006   0.091   1172
  Dihedral  :  5.295  48.848    987
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 27.34 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.54 (0.30), residues: 790
  helix:  1.30 (0.26), residues: 404
  sheet:  1.71 (0.75), residues: 46
  loop : -1.00 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 610 
 HIS   0.008   0.001   HIS A 373 
 PHE   0.036   0.002   PHE A 525 
 TYR   0.024   0.001   TYR B 380 
 ARG   0.017   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00963 (    6)
  link_NAG-ASN         : angle       3.93646 (   18)
  hydrogen bonds       : bond        0.04403 (  320)
  hydrogen bonds       : angle       5.08434 (  931)
  metal coordination   : bond        0.00297 (    2)
  SS BOND              : bond        0.00615 (    7)
  SS BOND              : angle       2.01230 (   14)
  covalent geometry    : bond        0.00316 ( 6690)
  covalent geometry    : angle       0.68484 ( 9097)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A   89 GLN cc_start: 0.6904 (mp10) cc_final: 0.6703 (mp10)
REVERT: A  131 LYS cc_start: 0.8320 (ptmm) cc_final: 0.7764 (ttmm)
REVERT: A  190 MET cc_start: 0.7604 (tmm) cc_final: 0.7363 (tmm)
REVERT: A  201 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7242 (m-30)
REVERT: A  202 TYR cc_start: 0.8217 (t80) cc_final: 0.7810 (t80)
REVERT: A  271 TRP cc_start: 0.8415 (m-90) cc_final: 0.7987 (m-90)
REVERT: A  432 ASN cc_start: 0.6861 (m-40) cc_final: 0.6269 (p0)
REVERT: A  455 MET cc_start: 0.7546 (tpt) cc_final: 0.6480 (tpt)
REVERT: A  476 LYS cc_start: 0.7468 (tptm) cc_final: 0.7157 (tppp)
REVERT: A  480 MET cc_start: 0.6350 (ttm) cc_final: 0.5993 (ttm)
REVERT: A  483 GLU cc_start: 0.7135 (tp30) cc_final: 0.6903 (mp0)
REVERT: A  509 ASP cc_start: 0.6663 (t70) cc_final: 0.6365 (t70)
REVERT: A  518 ARG cc_start: 0.7048 (ttp80) cc_final: 0.6772 (ttp80)
REVERT: A  536 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6201 (mt-10)
REVERT: A  582 ARG cc_start: 0.6782 (mmm160) cc_final: 0.6552 (mmm160)
REVERT: B  430 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7872 (t)
REVERT: B  454 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.8009 (ttm-80)
REVERT: B  498 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7856 (mtt90)
  outliers start: 17
  outliers final: 9
  residues processed: 197
  average time/residue: 1.1103
  time to fit residues: 230.3158
Evaluate side-chains
  191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  454 ARG
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  498 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 21 optimal weight:    0.0970
   chunk 66 optimal weight:    0.0040
   chunk 40 optimal weight:    0.0870
   chunk 6 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.1980
   overall best weight:    0.1168

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
B 487 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.176946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.162584 restraints weight = 20976.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.4228 rms_B_bonded: 4.02
r_work: 0.4087 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.4087
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4083 r_free = 0.4083    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4083 r_free = 0.4083    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.4614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6705  Z= 0.146
  Angle     :  0.704  10.485   9129  Z= 0.355
  Chirality :  0.047   0.356    968
  Planarity :  0.005   0.061   1172
  Dihedral  :  5.364  54.586    987
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 28.78 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.30), residues: 790
  helix:  1.37 (0.26), residues: 397
  sheet:  1.74 (0.73), residues: 46
  loop : -0.91 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 373 
 PHE   0.035   0.002   PHE A 369 
 TYR   0.020   0.001   TYR B 380 
 ARG   0.016   0.001   ARG A 582 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00916 (    6)
  link_NAG-ASN         : angle       3.97424 (   18)
  hydrogen bonds       : bond        0.04501 (  320)
  hydrogen bonds       : angle       5.05091 (  931)
  metal coordination   : bond        0.00080 (    2)
  SS BOND              : bond        0.00631 (    7)
  SS BOND              : angle       1.91296 (   14)
  covalent geometry    : bond        0.00327 ( 6690)
  covalent geometry    : angle       0.67900 ( 9097)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7993.36 seconds
wall clock time: 145 minutes 33.62 seconds (8733.62 seconds total)