Starting phenix.real_space_refine
on Wed Sep 17 18:50:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xn3_38496/09_2025/8xn3_38496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xn3_38496/09_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_38496/09_2025/8xn3_38496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xn3_38496/09_2025/8xn3_38496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xn3_38496/09_2025/8xn3_38496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xn3_38496/09_2025/8xn3_38496.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.55, per 1000 atoms: 0.39
  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: 0.53
  Conformation dependent library (CDL) restraints added in 438.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  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: 0.19
  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: 0.95

  Time building geometry restraints manager: 0.73 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:             13.340
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.150
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:6.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.330
-------------------------------------------------------------------------------
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 : 9.13
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (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
 ARG   0.002   0.000   ARG B 357 
 TYR   0.020   0.001   TYR A 385 
 PHE   0.019   0.001   PHE A 400 
 TRP   0.012   0.001   TRP A 566 
 HIS   0.013   0.002   HIS A 378 

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

*********************** 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  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 TYR cc_start: 0.6241 (t80) cc_final: 0.5812 (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: 0.7175 (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: 0.6041 (mmtm)
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: 0.7542 (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  369 PHE cc_start: 0.7415 (t80) cc_final: 0.7200 (t80)
REVERT: A  397 ASN cc_start: 0.7184 (p0) cc_final: 0.6923 (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: 0.7109 (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: 0.6411 (mtt180)
REVERT: A  483 GLU cc_start: 0.6695 (tp30) cc_final: 0.6375 (tp30)
REVERT: A  488 VAL cc_start: 0.7340 (p) cc_final: 0.6416 (t)
REVERT: A  489 GLU cc_start: 0.6545 (pm20) cc_final: 0.5325 (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: 0.6121 (p)
REVERT: A  610 TRP cc_start: 0.7239 (t60) cc_final: 0.6922 (t60)
REVERT: A  613 TYR cc_start: 0.6606 (p90) cc_final: 0.6283 (p90)
REVERT: B  396 TYR cc_start: 0.6643 (m-80) cc_final: 0.6021 (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  457 ARG cc_start: 0.6349 (ttt-90) cc_final: 0.6017 (ttp-170)
REVERT: B  459 SER cc_start: 0.6557 (p) cc_final: 0.6308 (m)
REVERT: B  462 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7521 (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: 0.4971
  time to fit residues: 118.5968
Evaluate side-chains
  199 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 194 ASN
A 340 GLN
A 345 HIS
A 601 ASN
B 354 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 505 HIS ** 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 = 0.4366 r_free = 0.4366 target = 0.175466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.160802 restraints weight = 22468.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.4221 rms_B_bonded: 4.19
r_work: 0.4063 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4047 r_free = 0.4047    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4047 r_free = 0.4047    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.2153

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= 0.185
  Angle     :  0.632   9.902   9129  Z= 0.321
  Chirality :  0.050   0.380    968
  Planarity :  0.005   0.044   1172
  Dihedral  :  5.852  48.792    987
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.95 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.30), residues: 790
  helix:  1.49 (0.26), residues: 401
  sheet:  1.37 (0.80), residues: 48
  loop : -0.58 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.017   0.002   TYR A 385 
 PHE   0.019   0.002   PHE A 230 
 TRP   0.023   0.002   TRP A 302 
 HIS   0.006   0.002   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6690)
  covalent geometry    : angle       0.60379 ( 9097)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       1.01700 (   14)
  hydrogen bonds       : bond        0.05282 (  320)
  hydrogen bonds       : angle       4.70694 (  931)
  metal coordination   : bond        0.00645 (    2)
  link_NAG-ASN         : bond        0.00939 (    6)
  link_NAG-ASN         : angle       4.18181 (   18)

*********************** 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
  219 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 202
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6457 (mm)
REVERT: A   63 ASN cc_start: 0.7608 (m-40) cc_final: 0.7086 (m-40)
REVERT: A  190 MET cc_start: 0.7692 (tmm) cc_final: 0.7466 (tmm)
REVERT: A  202 TYR cc_start: 0.8238 (t80) cc_final: 0.7962 (t80)
REVERT: A  482 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7648 (mtt180)
REVERT: A  483 GLU cc_start: 0.7503 (tp30) cc_final: 0.7273 (tp30)
REVERT: A  514 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7658 (mtm-85)
REVERT: A  518 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7063 (ttp80)
REVERT: B  494 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (t)
REVERT: B  509 ARG cc_start: 0.8300 (mtt180) cc_final: 0.8057 (mtt180)
  outliers start: 17
  outliers final: 6
  residues processed: 207
  average time/residue: 0.5689
  time to fit residues: 123.6778
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  : 0.244 
-------------------------------------------------------------------------------
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  320 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 HIS
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 69 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 71 optimal weight:    0.4980
   chunk 51 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0980
   chunk 76 optimal weight:    0.3980
   overall best weight:    0.2958

-------------------------------------------------------------------------------
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
A 442 GLN
A 472 GLN
B 360 ASN
B 409 GLN
B 414 GLN
B 493 GLN
** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.177140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.162258 restraints weight = 21634.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.4187 rms_B_bonded: 4.15
r_work: 0.4033 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4031 r_free = 0.4031    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4031 r_free = 0.4031    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6705  Z= 0.176
  Angle     :  0.634  10.043   9129  Z= 0.323
  Chirality :  0.050   0.439    968
  Planarity :  0.005   0.044   1172
  Dihedral  :  5.680  44.259    987
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.12 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.30), residues: 790
  helix:  1.46 (0.26), residues: 401
  sheet:  1.39 (0.77), residues: 49
  loop : -0.65 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 582 
 TYR   0.018   0.002   TYR A 613 
 PHE   0.029   0.002   PHE A 369 
 TRP   0.021   0.002   TRP A 610 
 HIS   0.006   0.002   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6690)
  covalent geometry    : angle       0.60328 ( 9097)
  SS BOND              : bond        0.00306 (    7)
  SS BOND              : angle       0.95529 (   14)
  hydrogen bonds       : bond        0.05084 (  320)
  hydrogen bonds       : angle       4.78163 (  931)
  metal coordination   : bond        0.00136 (    2)
  link_NAG-ASN         : bond        0.01463 (    6)
  link_NAG-ASN         : angle       4.41705 (   18)

*********************** 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
  213 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 193
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7958 (mm-40)
REVERT: A  201 ASP cc_start: 0.7783 (m-30) cc_final: 0.7357 (m-30)
REVERT: A  202 TYR cc_start: 0.8243 (t80) cc_final: 0.7817 (t80)
REVERT: A  482 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7617 (mtt180)
REVERT: A  483 GLU cc_start: 0.7499 (tp30) cc_final: 0.7289 (tp30)
REVERT: A  489 GLU cc_start: 0.6929 (pm20) cc_final: 0.6511 (pm20)
REVERT: A  514 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7745 (mtm-85)
REVERT: A  518 ARG cc_start: 0.7320 (ttp80) cc_final: 0.6993 (ttp80)
REVERT: B  396 TYR cc_start: 0.7041 (m-80) cc_final: 0.6535 (m-80)
REVERT: B  509 ARG cc_start: 0.8330 (mtt180) cc_final: 0.8102 (mtt180)
  outliers start: 20
  outliers final: 6
  residues processed: 201
  average time/residue: 0.5356
  time to fit residues: 113.4932
Evaluate side-chains
  194 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 187
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  401 HIS
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 47 optimal weight:    0.1980
   chunk 44 optimal weight:    0.0970
   chunk 64 optimal weight:    0.1980
   chunk 74 optimal weight:    0.1980
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.1978

-------------------------------------------------------------------------------
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
A 556 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 506 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 = 0.4379 r_free = 0.4379 target = 0.178344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.163179 restraints weight = 23197.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 4.28
r_work: 0.4044 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4045 r_free = 0.4045    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.3286

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= 0.150
  Angle     :  0.636   9.818   9129  Z= 0.326
  Chirality :  0.049   0.411    968
  Planarity :  0.005   0.042   1172
  Dihedral  :  5.474  46.177    987
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.27 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.30), residues: 790
  helix:  1.43 (0.26), residues: 398
  sheet:  1.18 (0.74), residues: 49
  loop : -0.65 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 582 
 TYR   0.027   0.002   TYR B 380 
 PHE   0.028   0.002   PHE A 369 
 TRP   0.027   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6690)
  covalent geometry    : angle       0.60640 ( 9097)
  SS BOND              : bond        0.00340 (    7)
  SS BOND              : angle       0.92699 (   14)
  hydrogen bonds       : bond        0.04756 (  320)
  hydrogen bonds       : angle       4.79657 (  931)
  metal coordination   : bond        0.00032 (    2)
  link_NAG-ASN         : bond        0.01220 (    6)
  link_NAG-ASN         : angle       4.32241 (   18)

*********************** 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
  215 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 189
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6448 (mt)
REVERT: A  131 LYS cc_start: 0.8403 (ptmm) cc_final: 0.7576 (ttmm)
REVERT: A  201 ASP cc_start: 0.7838 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  202 TYR cc_start: 0.8269 (t80) cc_final: 0.7846 (t80)
REVERT: A  455 MET cc_start: 0.7921 (tpt) cc_final: 0.7326 (tpt)
REVERT: A  482 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7665 (mtt180)
REVERT: A  483 GLU cc_start: 0.7538 (tp30) cc_final: 0.7320 (tp30)
REVERT: A  488 VAL cc_start: 0.8046 (p) cc_final: 0.7777 (t)
REVERT: A  489 GLU cc_start: 0.7003 (pm20) cc_final: 0.6416 (pm20)
REVERT: A  514 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (mtm180)
REVERT: A  518 ARG cc_start: 0.7144 (ttp80) cc_final: 0.6832 (ttp80)
REVERT: A  613 TYR cc_start: 0.7081 (p90) cc_final: 0.6397 (p90)
REVERT: B  454 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7975 (ttm-80)
REVERT: B  509 ARG cc_start: 0.8282 (mtt180) cc_final: 0.8055 (mtt180)
  outliers start: 26
  outliers final: 13
  residues processed: 196
  average time/residue: 0.5099
  time to fit residues: 105.2863
Evaluate side-chains
  202 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   26 LYS
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue   75 GLU
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  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  514 ARG
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  459 SER
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  494 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 74 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    0.1980
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0870
   chunk 29 optimal weight:    0.0970
   overall best weight:    0.1556

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 345 HIS
B 417 ASN
** B 505 HIS ** 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 = 0.4380 r_free = 0.4380 target = 0.178661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.165749 restraints weight = 15454.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 3.17
r_work: 0.4110 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4112
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4112 r_free = 0.4112    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4112 r_free = 0.4112    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4112
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6705  Z= 0.138
  Angle     :  0.639   9.633   9129  Z= 0.320
  Chirality :  0.048   0.406    968
  Planarity :  0.005   0.048   1172
  Dihedral  :  5.376  50.862    987
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.01 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.30), residues: 790
  helix:  1.45 (0.26), residues: 398
  sheet:  1.30 (0.76), residues: 49
  loop : -0.70 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 582 
 TYR   0.020   0.002   TYR B 380 
 PHE   0.032   0.002   PHE A 369 
 TRP   0.035   0.002   TRP A 610 
 HIS   0.005   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6690)
  covalent geometry    : angle       0.61061 ( 9097)
  SS BOND              : bond        0.00241 (    7)
  SS BOND              : angle       0.82175 (   14)
  hydrogen bonds       : bond        0.04552 (  320)
  hydrogen bonds       : angle       4.78166 (  931)
  metal coordination   : bond        0.00028 (    2)
  link_NAG-ASN         : bond        0.01214 (    6)
  link_NAG-ASN         : angle       4.23492 (   18)

*********************** 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
  216 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 195
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6327 (mt)
REVERT: A   62 MET cc_start: 0.8318 (ttp) cc_final: 0.8113 (ttp)
REVERT: A   98 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7890 (mm-40)
REVERT: A  131 LYS cc_start: 0.8358 (ptmm) cc_final: 0.7787 (ttmm)
REVERT: A  190 MET cc_start: 0.7672 (tmm) cc_final: 0.7428 (tmm)
REVERT: A  201 ASP cc_start: 0.7792 (m-30) cc_final: 0.7524 (m-30)
REVERT: A  202 TYR cc_start: 0.8216 (t80) cc_final: 0.7799 (t80)
REVERT: A  455 MET cc_start: 0.7749 (tpt) cc_final: 0.7370 (tpt)
REVERT: A  481 LYS cc_start: 0.7789 (tttp) cc_final: 0.7589 (tttm)
REVERT: A  482 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7654 (mtt180)
REVERT: A  483 GLU cc_start: 0.7300 (tp30) cc_final: 0.7087 (tp30)
REVERT: A  488 VAL cc_start: 0.8009 (p) cc_final: 0.7781 (t)
REVERT: A  518 ARG cc_start: 0.7099 (ttp80) cc_final: 0.6779 (ttp80)
REVERT: B  454 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8021 (ttm-80)
  outliers start: 21
  outliers final: 10
  residues processed: 203
  average time/residue: 0.5046
  time to fit residues: 107.5885
Evaluate side-chains
  195 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  198 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  483 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0770
   chunk 10 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0070
   chunk 30 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.2556

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 137 ASN
A 345 HIS
B 417 ASN
B 448 ASN
B 450 ASN
** B 505 HIS ** 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 = 0.4365 r_free = 0.4365 target = 0.177412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.162195 restraints weight = 21965.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.4185 rms_B_bonded: 4.26
r_work: 0.4034 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4037
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4037 r_free = 0.4037    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4037 r_free = 0.4037    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4037
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6705  Z= 0.167
  Angle     :  0.680   9.773   9129  Z= 0.344
  Chirality :  0.049   0.400    968
  Planarity :  0.005   0.062   1172
  Dihedral  :  5.358  45.376    987
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 21.87 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.30), residues: 790
  helix:  1.36 (0.26), residues: 398
  sheet:  1.08 (0.74), residues: 51
  loop : -0.81 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 582 
 TYR   0.021   0.002   TYR B 380 
 PHE   0.040   0.002   PHE A 369 
 TRP   0.036   0.002   TRP A 610 
 HIS   0.007   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6690)
  covalent geometry    : angle       0.65283 ( 9097)
  SS BOND              : bond        0.00421 (    7)
  SS BOND              : angle       1.23561 (   14)
  hydrogen bonds       : bond        0.04824 (  320)
  hydrogen bonds       : angle       4.89127 (  931)
  metal coordination   : bond        0.00143 (    2)
  link_NAG-ASN         : bond        0.01175 (    6)
  link_NAG-ASN         : angle       4.21711 (   18)

*********************** 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
  213 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 189
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6364 (mp)
REVERT: A   98 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7988 (mm-40)
REVERT: A  131 LYS cc_start: 0.8352 (ptmm) cc_final: 0.7648 (ttmm)
REVERT: A  190 MET cc_start: 0.7760 (tmm) cc_final: 0.7542 (tmt)
REVERT: A  202 TYR cc_start: 0.8293 (t80) cc_final: 0.7847 (t80)
REVERT: A  238 GLU cc_start: 0.6889 (tp30) cc_final: 0.6667 (tp30)
REVERT: A  455 MET cc_start: 0.7855 (tpt) cc_final: 0.7494 (tpt)
REVERT: A  482 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7732 (mtt180)
REVERT: A  483 GLU cc_start: 0.7489 (tp30) cc_final: 0.7273 (tp30)
REVERT: A  488 VAL cc_start: 0.8104 (p) cc_final: 0.7868 (t)
REVERT: A  518 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6887 (ttp80)
REVERT: A  582 ARG cc_start: 0.7039 (mmm160) cc_final: 0.6735 (mmm160)
REVERT: B  396 TYR cc_start: 0.7111 (m-80) cc_final: 0.6562 (m-80)
REVERT: B  454 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8155 (ttm-80)
REVERT: B  495 TYR cc_start: 0.7380 (m-80) cc_final: 0.6982 (m-10)
REVERT: B  498 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8135 (mtt90)
  outliers start: 24
  outliers final: 9
  residues processed: 202
  average time/residue: 0.5250
  time to fit residues: 111.6293
Evaluate side-chains
  194 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 183
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  233 ILE
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 B residue  417 ASN
Chi-restraints excluded: chain B residue  430 THR
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 9 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 71 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 44 optimal weight:    0.0870
   chunk 46 optimal weight:    0.1980
   chunk 59 optimal weight:    0.0470
   chunk 63 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0770
   overall best weight:    0.1414

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 345 HIS
B 448 ASN
** B 505 HIS ** 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 = 0.4388 r_free = 0.4388 target = 0.179354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.164400 restraints weight = 20740.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 3.99
r_work: 0.4070 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.3934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6705  Z= 0.138
  Angle     :  0.652   9.496   9129  Z= 0.331
  Chirality :  0.047   0.372    968
  Planarity :  0.005   0.047   1172
  Dihedral  :  5.292  50.661    987
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 23.31 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.30), residues: 790
  helix:  1.41 (0.26), residues: 396
  sheet:  1.06 (0.75), residues: 51
  loop : -0.80 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 582 
 TYR   0.021   0.001   TYR A  50 
 PHE   0.039   0.002   PHE A 369 
 TRP   0.038   0.002   TRP A 610 
 HIS   0.005   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6690)
  covalent geometry    : angle       0.62563 ( 9097)
  SS BOND              : bond        0.00232 (    7)
  SS BOND              : angle       1.09037 (   14)
  hydrogen bonds       : bond        0.04466 (  320)
  hydrogen bonds       : angle       4.88082 (  931)
  metal coordination   : bond        0.00069 (    2)
  link_NAG-ASN         : bond        0.01175 (    6)
  link_NAG-ASN         : angle       4.11781 (   18)

*********************** 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: 23
    poor density    : 197
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LYS cc_start: 0.8288 (ptmm) cc_final: 0.7711 (ttmm)
REVERT: A  190 MET cc_start: 0.7710 (tmm) cc_final: 0.7492 (tmt)
REVERT: A  202 TYR cc_start: 0.8233 (t80) cc_final: 0.7849 (t80)
REVERT: A  271 TRP cc_start: 0.8361 (m-90) cc_final: 0.7884 (m-90)
REVERT: A  307 ILE cc_start: 0.8232 (mt) cc_final: 0.7985 (mt)
REVERT: A  330 ASN cc_start: 0.7295 (m110) cc_final: 0.7090 (m110)
REVERT: A  455 MET cc_start: 0.7827 (tpt) cc_final: 0.7464 (tpt)
REVERT: A  482 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7703 (mtt180)
REVERT: A  483 GLU cc_start: 0.7487 (tp30) cc_final: 0.7270 (tp30)
REVERT: A  488 VAL cc_start: 0.8006 (p) cc_final: 0.7759 (t)
REVERT: A  518 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6818 (ttp80)
REVERT: B  430 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7772 (t)
REVERT: B  495 TYR cc_start: 0.7275 (m-80) cc_final: 0.6860 (m-10)
REVERT: B  498 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8058 (mtt90)
REVERT: B  509 ARG cc_start: 0.8399 (mtt-85) cc_final: 0.8194 (mmt90)
  outliers start: 23
  outliers final: 12
  residues processed: 208
  average time/residue: 0.5255
  time to fit residues: 115.4488
Evaluate side-chains
  200 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
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  320 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  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  483 VAL
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 0 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0030
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0470
   chunk 18 optimal weight:    0.3980
   chunk 65 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 43 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.2888

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN
B 450 ASN
** B 505 HIS ** 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 = 0.4349 r_free = 0.4349 target = 0.174212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.158649 restraints weight = 23491.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.4173 rms_B_bonded: 4.38
r_work: 0.4015 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4014 r_free = 0.4014    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4014 r_free = 0.4014    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   6705  Z= 0.184
  Angle     :  0.720   9.894   9129  Z= 0.369
  Chirality :  0.050   0.377    968
  Planarity :  0.006   0.065   1172
  Dihedral  :  5.394  42.966    987
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 24.46 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.30), residues: 790
  helix:  1.17 (0.26), residues: 401
  sheet:  1.07 (0.77), residues: 51
  loop : -0.93 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 582 
 TYR   0.028   0.002   TYR A  50 
 PHE   0.039   0.002   PHE A 369 
 TRP   0.040   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6690)
  covalent geometry    : angle       0.69101 ( 9097)
  SS BOND              : bond        0.00657 (    7)
  SS BOND              : angle       2.08404 (   14)
  hydrogen bonds       : bond        0.04922 (  320)
  hydrogen bonds       : angle       5.07924 (  931)
  metal coordination   : bond        0.00403 (    2)
  link_NAG-ASN         : bond        0.01105 (    6)
  link_NAG-ASN         : angle       4.22956 (   18)

*********************** 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
  208 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 187
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7949 (mm-40)
REVERT: A  123 MET cc_start: 0.7431 (mtt) cc_final: 0.6932 (mtt)
REVERT: A  129 THR cc_start: 0.7704 (p) cc_final: 0.7482 (t)
REVERT: A  131 LYS cc_start: 0.8311 (ptmm) cc_final: 0.7670 (ttmm)
REVERT: A  190 MET cc_start: 0.7738 (tmm) cc_final: 0.7507 (tmm)
REVERT: A  202 TYR cc_start: 0.8280 (t80) cc_final: 0.7838 (t80)
REVERT: A  238 GLU cc_start: 0.6975 (tp30) cc_final: 0.6747 (tp30)
REVERT: A  271 TRP cc_start: 0.8448 (m-90) cc_final: 0.7993 (m-90)
REVERT: A  455 MET cc_start: 0.7856 (tpt) cc_final: 0.7510 (tpt)
REVERT: A  476 LYS cc_start: 0.7592 (tptm) cc_final: 0.7304 (tppp)
REVERT: A  482 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7752 (mtt180)
REVERT: A  483 GLU cc_start: 0.7579 (tp30) cc_final: 0.7363 (tp30)
REVERT: A  488 VAL cc_start: 0.8129 (p) cc_final: 0.7889 (t)
REVERT: A  518 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6896 (ttp80)
REVERT: B  396 TYR cc_start: 0.7083 (m-80) cc_final: 0.6604 (m-80)
REVERT: B  430 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7878 (t)
REVERT: B  454 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8137 (ttm-80)
REVERT: B  495 TYR cc_start: 0.7393 (m-80) cc_final: 0.6995 (m-10)
REVERT: B  498 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8207 (mtt90)
  outliers start: 21
  outliers final: 12
  residues processed: 200
  average time/residue: 0.5045
  time to fit residues: 106.3290
Evaluate side-chains
  198 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  143 LEU
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  290 ASN
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  472 ILE
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 59 optimal weight:    0.0170
   chunk 6 optimal weight:    0.0000
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0770
   chunk 66 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0870
   chunk 36 optimal weight:    0.0770
   chunk 33 optimal weight:    0.0970
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0770
   overall best weight:    0.0496

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

Flipped N/Q/H residues before XYZ refinement:
A 535 HIS
B 448 ASN
** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.179454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.163063 restraints weight = 27460.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.4225 rms_B_bonded: 4.87
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4226 r_free = 0.4226    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4226 r_free = 0.4226    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.4314

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= 0.135
  Angle     :  0.670   9.387   9129  Z= 0.342
  Chirality :  0.047   0.339    968
  Planarity :  0.005   0.041   1172
  Dihedral  :  5.411  59.704    987
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 26.47 %
    Favored  : 71.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.30), residues: 790
  helix:  1.35 (0.26), residues: 401
  sheet:  1.61 (0.76), residues: 45
  loop : -0.91 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 357 
 TYR   0.029   0.001   TYR B 380 
 PHE   0.038   0.002   PHE A 369 
 TRP   0.041   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6690)
  covalent geometry    : angle       0.64318 ( 9097)
  SS BOND              : bond        0.00617 (    7)
  SS BOND              : angle       1.96204 (   14)
  hydrogen bonds       : bond        0.04089 (  320)
  hydrogen bonds       : angle       5.01445 (  931)
  metal coordination   : bond        0.00450 (    2)
  link_NAG-ASN         : bond        0.01130 (    6)
  link_NAG-ASN         : angle       3.95494 (   18)

*********************** 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
  200 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 187
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7456 (mm-40)
REVERT: A  131 LYS cc_start: 0.7932 (ptmm) cc_final: 0.7605 (ttmm)
REVERT: A  202 TYR cc_start: 0.7898 (t80) cc_final: 0.7593 (t80)
REVERT: A  271 TRP cc_start: 0.8470 (m-90) cc_final: 0.8056 (m-90)
REVERT: A  307 ILE cc_start: 0.7784 (mt) cc_final: 0.7344 (mt)
REVERT: A  432 ASN cc_start: 0.6686 (m-40) cc_final: 0.6046 (p0)
REVERT: A  455 MET cc_start: 0.7205 (tpt) cc_final: 0.6868 (tpt)
REVERT: A  476 LYS cc_start: 0.7588 (tptm) cc_final: 0.7247 (tppp)
REVERT: A  483 GLU cc_start: 0.7355 (tp30) cc_final: 0.7109 (tp30)
REVERT: A  488 VAL cc_start: 0.7893 (p) cc_final: 0.7673 (t)
REVERT: A  518 ARG cc_start: 0.6618 (ttp80) cc_final: 0.6383 (ttp80)
REVERT: B  430 THR cc_start: 0.7903 (OUTLIER) cc_final: 0.7622 (t)
REVERT: B  495 TYR cc_start: 0.7163 (m-80) cc_final: 0.6646 (m-10)
  outliers start: 13
  outliers final: 6
  residues processed: 194
  average time/residue: 0.4938
  time to fit residues: 101.1337
Evaluate side-chains
  183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 176
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  233 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  459 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0270
   chunk 9 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 52 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0980
   chunk 38 optimal weight:    0.0270
   chunk 74 optimal weight:    0.0770
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.1254

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.178200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.167838 restraints weight = 10146.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.4279 rms_B_bonded: 2.26
r_work: 0.4191 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.4062 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4064 r_free = 0.4064    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4064 r_free = 0.4064    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6705  Z= 0.145
  Angle     :  0.703   9.876   9129  Z= 0.357
  Chirality :  0.048   0.349    968
  Planarity :  0.005   0.070   1172
  Dihedral  :  5.460  58.846    987
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 28.92 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.30), residues: 790
  helix:  1.35 (0.26), residues: 397
  sheet:  1.71 (0.76), residues: 45
  loop : -0.87 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 582 
 TYR   0.024   0.002   TYR B 380 
 PHE   0.037   0.002   PHE A 369 
 TRP   0.043   0.002   TRP A 610 
 HIS   0.008   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6690)
  covalent geometry    : angle       0.67768 ( 9097)
  SS BOND              : bond        0.00586 (    7)
  SS BOND              : angle       1.71859 (   14)
  hydrogen bonds       : bond        0.04367 (  320)
  hydrogen bonds       : angle       5.02552 (  931)
  metal coordination   : bond        0.00242 (    2)
  link_NAG-ASN         : bond        0.01126 (    6)
  link_NAG-ASN         : angle       4.00181 (   18)

********************** 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
  188 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 181
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.8224 (tp-100) cc_final: 0.8011 (mm-40)
REVERT: A  131 LYS cc_start: 0.8121 (ptmm) cc_final: 0.7714 (ttmm)
REVERT: A  202 TYR cc_start: 0.8244 (t80) cc_final: 0.7860 (t80)
REVERT: A  307 ILE cc_start: 0.7981 (mt) cc_final: 0.7563 (mt)
REVERT: A  357 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7344 (mtt-85)
REVERT: A  393 ARG cc_start: 0.7650 (mtt90) cc_final: 0.7395 (mtt90)
REVERT: A  432 ASN cc_start: 0.6934 (m-40) cc_final: 0.6467 (p0)
REVERT: A  455 MET cc_start: 0.7869 (tpt) cc_final: 0.7492 (tpp)
REVERT: A  476 LYS cc_start: 0.7491 (tptm) cc_final: 0.7175 (tppp)
REVERT: A  480 MET cc_start: 0.6384 (ttm) cc_final: 0.6162 (ptp)
REVERT: A  483 GLU cc_start: 0.7467 (tp30) cc_final: 0.7250 (tp30)
REVERT: A  518 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6866 (ttp80)
REVERT: A  582 ARG cc_start: 0.7076 (mmm160) cc_final: 0.6742 (mmm160)
REVERT: B  430 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7889 (t)
REVERT: B  495 TYR cc_start: 0.7248 (m-80) cc_final: 0.6780 (m-10)
  outliers start: 7
  outliers final: 5
  residues processed: 185
  average time/residue: 0.4910
  time to fit residues: 95.9178
Evaluate side-chains
  184 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 178
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
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  233 ILE
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 68 optimal weight:    0.1980
   chunk 20 optimal weight:    0.2980
   chunk 15 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0470
   chunk 51 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 10 optimal weight:    0.1980
   chunk 67 optimal weight:    0.0980
   overall best weight:    0.1278

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

Flipped N/Q/H residues before XYZ refinement:
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.178734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.163795 restraints weight = 20790.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.4237 rms_B_bonded: 4.10
r_work: 0.4096 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4099
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4099 r_free = 0.4099    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4099 r_free = 0.4099    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4099
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6904
moved from start:          0.4485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6705  Z= 0.149
  Angle     :  0.720   9.756   9129  Z= 0.368
  Chirality :  0.048   0.343    968
  Planarity :  0.005   0.075   1172
  Dihedral  :  5.483  58.045    987
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 29.78 %
    Favored  : 69.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.29), residues: 790
  helix:  1.30 (0.26), residues: 398
  sheet:  1.83 (0.76), residues: 45
  loop : -0.88 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 582 
 TYR   0.021   0.001   TYR A  50 
 PHE   0.037   0.002   PHE A 369 
 TRP   0.043   0.002   TRP A 610 
 HIS   0.005   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6690)
  covalent geometry    : angle       0.69582 ( 9097)
  SS BOND              : bond        0.00544 (    7)
  SS BOND              : angle       1.69304 (   14)
  hydrogen bonds       : bond        0.04337 (  320)
  hydrogen bonds       : angle       5.00093 (  931)
  metal coordination   : bond        0.00236 (    2)
  link_NAG-ASN         : bond        0.01136 (    6)
  link_NAG-ASN         : angle       3.97850 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3559.87 seconds
wall clock time: 61 minutes 10.62 seconds (3670.62 seconds total)