Starting phenix.real_space_refine
on Sat May 10 09:23:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yht_39300/05_2025/8yht_39300.cif"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3724      2.51       5
     N     972      2.21       5
     O    1129      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5845
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5323
          Classifications: {'peptide': 663}
          Link IDs: {'PTRANS': 26, 'TRANS': 636}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 326
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 6.09, per 1000 atoms: 1.04
  Number of scatterers: 5845
  At special positions: 0
  Unit cell: (52.456, 102.92, 111.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1129      8.00
     N     972      7.00
     C    3724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 651 " - pdb=" SG  CYS A 696 " distance=2.03

  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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  52 "
      " NAG A 802 " - " ASN A  57 "
      " NAG A 803 " - " ASN A 124 "
      " NAG A 804 " - " ASN A 252 "
      " NAG A 805 " - " ASN A 275 "
      " NAG A 806 " - " ASN A 291 "
      " NAG C   1 " - " ASN A 247 "
      " NAG D   1 " - " ASN A 265 "
      " NAG E   1 " - " ASN A 398 "
      " NAG F   1 " - " ASN A 413 "
  Time building additional restraints: 1.70
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 6 sheets defined
      15.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.681A  pdb=" N   ARG A  73 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 4.612A  pdb=" N   ILE A 193 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.850A  pdb=" N   TRP A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 4.166A  pdb=" N   LEU A 318 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 319 " --> pdb=" O   HIS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.591A  pdb=" N   THR A 400 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE A 401 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   VAL A 402 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   SER A 403 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 546
      removed outlier: 3.726A  pdb=" N   TRP A 546 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.569A  pdb=" N   TYR A 683 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS A 684 " --> pdb=" O   PRO A 681 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 680 through 684'
    Processing helix  chain 'A' and resid 687 through 691
    Processing helix  chain 'B' and resid 2 through 21
      removed outlier: 3.713A  pdb=" N   LEU B  11 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 40
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 4.413A  pdb=" N   THR A  29 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.629A  pdb=" N   LEU A 104 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 128 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335
      removed outlier: 6.879A  pdb=" N   ILE A 310 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 313 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.699A  pdb=" N   MET A 486 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER A 514 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446
      removed outlier: 6.915A  pdb=" N   GLN A 445 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 493 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)

    69 hydrogen bonds defined for protein.
    162 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1874
        1.34 -     1.46: 1285
        1.46 -     1.58: 2773
        1.58 -     1.70: 0
        1.70 -     1.82: 29
  Bond restraints: 5961
  Sorted by residual:
  bond pdb=" N   ASP A 292 "
       pdb=" CA  ASP A 292 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.29e+00
  bond pdb=" N   PHE A 294 "
       pdb=" CA  PHE A 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.62e+00
  bond pdb=" N   SER A 293 "
       pdb=" CA  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.31e-02 5.83e+03 3.96e+00
  bond pdb=" CA  SER A 293 "
       pdb=" CB  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.534  1.503  0.031 1.60e-02 3.91e+03 3.88e+00
  bond pdb=" C1  NAG A 805 "
       pdb=" O5  NAG A 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.06e+00
  ... (remaining 5956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 7741
        1.57 -     3.14: 291
        3.14 -     4.71: 43
        4.71 -     6.28: 9
        6.28 -     7.85: 1
  Bond angle restraints: 8085
  Sorted by residual:
  angle pdb=" N   ALA A 491 "
        pdb=" CA  ALA A 491 "
        pdb=" C   ALA A 491 "
      ideal   model   delta    sigma   weight residual
     108.63  103.06    5.57 1.60e+00 3.91e-01 1.21e+01
  angle pdb=" CA  SER A 293 "
        pdb=" C   SER A 293 "
        pdb=" O   SER A 293 "
      ideal   model   delta    sigma   weight residual
     121.68  117.84    3.84 1.18e+00 7.18e-01 1.06e+01
  angle pdb=" N   GLU B  15 "
        pdb=" CA  GLU B  15 "
        pdb=" CB  GLU B  15 "
      ideal   model   delta    sigma   weight residual
     110.16  114.68   -4.52 1.48e+00 4.57e-01 9.32e+00
  angle pdb=" CA  VAL A 144 "
        pdb=" C   VAL A 144 "
        pdb=" N   LYS A 145 "
      ideal   model   delta    sigma   weight residual
     116.60  120.92   -4.32 1.45e+00 4.76e-01 8.89e+00
  angle pdb=" C   PHE A 294 "
        pdb=" N   ALA A 295 "
        pdb=" CA  ALA A 295 "
      ideal   model   delta    sigma   weight residual
     120.99  115.82    5.17 1.86e+00 2.89e-01 7.72e+00
  ... (remaining 8080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.41: 3453
       21.41 -    42.83: 290
       42.83 -    64.24: 32
       64.24 -    85.66: 8
       85.66 -   107.07: 8
  Dihedral angle restraints: 3791
    sinusoidal: 1721
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CB  CYS A 651 "
           pdb=" SG  CYS A 651 "
           pdb=" SG  CYS A 696 "
           pdb=" CB  CYS A 696 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.59   80.41     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CB  CYS A 649 "
           pdb=" SG  CYS A 649 "
           pdb=" SG  CYS A 677 "
           pdb=" CB  CYS A 677 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.69   58.31     1      1.00e+01 1.00e-02 4.56e+01
  dihedral pdb=" CA  ASN A  61 "
           pdb=" C   ASN A  61 "
           pdb=" N   GLN A  62 "
           pdb=" CA  GLN A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 3788 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 634
       0.044 -    0.088: 275
       0.088 -    0.131: 59
       0.131 -    0.175: 6
       0.175 -    0.219: 2
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" C1  NAG A 806 "
            pdb=" ND2 ASN A 291 "
            pdb=" C2  NAG A 806 "
            pdb=" O5  NAG A 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 413 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CB  ILE A 591 "
            pdb=" CA  ILE A 591 "
            pdb=" CG1 ILE A 591 "
            pdb=" CG2 ILE A 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 973 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 668 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 669 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 669 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 669 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 291 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ASN A 291 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A 291 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 292 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 631 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 632 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 632 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 632 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 52
        2.58 -     3.16: 4839
        3.16 -     3.74: 8712
        3.74 -     4.32: 12137
        4.32 -     4.90: 19597
  Nonbonded interactions: 45337
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 416 "
            pdb=" OE2 GLU B  19 "
     model   vdw
     1.995 3.120
  nonbonded pdb=" O   GLU A 363 "
            pdb=" OG  SER A 389 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 387 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP A 648 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NZ  LYS A 201 "
            pdb=" OE2 GLU A 203 "
     model   vdw
     2.285 3.120
  ... (remaining 45332 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.960
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5979  Z= 0.195
  Angle     :  0.708   7.848   8135  Z= 0.361
  Chirality :  0.047   0.219    976
  Planarity :  0.004   0.043   1014
  Dihedral  : 15.457 107.071   2425
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.05 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.31 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.32), residues: 697
  helix: -0.67 (0.62), residues: 75
  sheet: -4.11 (0.49), residues: 74
  loop : -2.04 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.009   0.001   PHE A 119 
 TYR   0.020   0.002   TYR B   6 
 ARG   0.002   0.000   ARG A 689 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00291 (   10)
  link_NAG-ASN         : angle       1.78916 (   30)
  link_BETA1-4         : bond        0.00333 (    4)
  link_BETA1-4         : angle       0.89383 (   12)
  hydrogen bonds       : bond        0.23794 (   69)
  hydrogen bonds       : angle       6.97953 (  162)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       1.10141 (    8)
  covalent geometry    : bond        0.00398 ( 5961)
  covalent geometry    : angle       0.69978 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 157
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 160
  average time/residue: 0.8439
  time to fit residues: 143.5959
Evaluate side-chains
  68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 109 ASN
A 169 GLN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
A 365 ASN
A 538 GLN
A 541 ASN
A 550 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.145757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.118005 restraints weight = 14172.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.4362 rms_B_bonded: 5.56
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6653
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5979  Z= 0.158
  Angle     :  0.780  10.170   8135  Z= 0.373
  Chirality :  0.050   0.501    976
  Planarity :  0.004   0.047   1014
  Dihedral  : 10.089  83.964   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.91 %
    Favored  : 88.09 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 14.75 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.31), residues: 697
  helix: -0.58 (0.60), residues: 69
  sheet: -4.11 (0.45), residues: 80
  loop : -1.91 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 108 
 PHE   0.013   0.001   PHE A 574 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.004   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01208 (   10)
  link_NAG-ASN         : angle       2.58664 (   30)
  link_BETA1-4         : bond        0.00515 (    4)
  link_BETA1-4         : angle       1.38717 (   12)
  hydrogen bonds       : bond        0.05814 (   69)
  hydrogen bonds       : angle       6.08982 (  162)
  SS BOND              : bond        0.00263 (    4)
  SS BOND              : angle       1.65503 (    8)
  covalent geometry    : bond        0.00364 ( 5961)
  covalent geometry    : angle       0.76279 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8024 (mm)
REVERT: A  245 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8274 (mm)
REVERT: A  328 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6729 (t0)
REVERT: A  330 LYS cc_start: 0.7768 (tttm) cc_final: 0.7261 (tttp)
REVERT: A  347 ASP cc_start: 0.6132 (m-30) cc_final: 0.5707 (m-30)
REVERT: A  361 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.6373 (t0)
REVERT: A  363 GLU cc_start: 0.6737 (tp30) cc_final: 0.5793 (tp30)
REVERT: A  440 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8038 (mp)
REVERT: A  525 MET cc_start: 0.4772 (OUTLIER) cc_final: 0.3849 (mpt)
REVERT: A  585 LEU cc_start: 0.7934 (mt) cc_final: 0.7637 (mm)
REVERT: A  613 LYS cc_start: 0.8585 (mttt) cc_final: 0.8159 (mmmt)
REVERT: B   27 ARG cc_start: 0.9330 (mmp80) cc_final: 0.9029 (mmp80)
  outliers start: 24
  outliers final: 8
  residues processed: 96
  average time/residue: 0.8083
  time to fit residues: 83.0819
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.142704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.115557 restraints weight = 14181.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.4319 rms_B_bonded: 5.41
r_work (final): 0.4319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5979  Z= 0.183
  Angle     :  0.786   7.865   8135  Z= 0.375
  Chirality :  0.049   0.465    976
  Planarity :  0.004   0.051   1014
  Dihedral  :  8.597  63.557   1032
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.59 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.31), residues: 697
  helix: -0.60 (0.59), residues: 69
  sheet: -4.11 (0.45), residues: 80
  loop : -1.87 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 452 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.015   0.001   PHE A 119 
 TYR   0.016   0.002   TYR B   6 
 ARG   0.004   0.000   ARG B  12 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00855 (   10)
  link_NAG-ASN         : angle       2.26962 (   30)
  link_BETA1-4         : bond        0.00482 (    4)
  link_BETA1-4         : angle       1.36823 (   12)
  hydrogen bonds       : bond        0.05741 (   69)
  hydrogen bonds       : angle       5.86131 (  162)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       0.99203 (    8)
  covalent geometry    : bond        0.00429 ( 5961)
  covalent geometry    : angle       0.77361 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7893 (m-40) cc_final: 0.7494 (t0)
REVERT: A   94 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8095 (mm)
REVERT: A  203 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7251 (mp0)
REVERT: A  330 LYS cc_start: 0.7795 (tttm) cc_final: 0.7325 (tttp)
REVERT: A  347 ASP cc_start: 0.6352 (m-30) cc_final: 0.5941 (m-30)
REVERT: A  361 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6639 (t0)
REVERT: A  363 GLU cc_start: 0.6889 (tp30) cc_final: 0.5937 (tp30)
REVERT: A  525 MET cc_start: 0.4925 (OUTLIER) cc_final: 0.3744 (mpt)
REVERT: A  575 ASP cc_start: 0.7456 (m-30) cc_final: 0.7114 (m-30)
REVERT: A  585 LEU cc_start: 0.8103 (mt) cc_final: 0.7854 (mm)
REVERT: A  613 LYS cc_start: 0.8602 (mttt) cc_final: 0.8220 (mmmt)
REVERT: B    8 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8921 (ptpt)
REVERT: B   27 ARG cc_start: 0.9321 (mmp80) cc_final: 0.9056 (mmp80)
REVERT: B   31 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8701 (mm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 84
  average time/residue: 0.7624
  time to fit residues: 68.8284
Evaluate side-chains
  78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  486 MET
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 42 optimal weight:    0.0670
   chunk 56 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 57 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.143716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.116889 restraints weight = 14763.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.4343 rms_B_bonded: 5.51
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5979  Z= 0.145
  Angle     :  0.765  17.414   8135  Z= 0.352
  Chirality :  0.047   0.423    976
  Planarity :  0.004   0.053   1014
  Dihedral  :  7.471  53.950   1032
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.12 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.31), residues: 697
  helix: -0.41 (0.60), residues: 69
  sheet: -4.12 (0.46), residues: 75
  loop : -1.93 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 108 
 PHE   0.012   0.001   PHE A 119 
 TYR   0.015   0.002   TYR B   5 
 ARG   0.004   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00733 (   10)
  link_NAG-ASN         : angle       2.11929 (   30)
  link_BETA1-4         : bond        0.00465 (    4)
  link_BETA1-4         : angle       1.53545 (   12)
  hydrogen bonds       : bond        0.04894 (   69)
  hydrogen bonds       : angle       5.55601 (  162)
  SS BOND              : bond        0.00251 (    4)
  SS BOND              : angle       1.56487 (    8)
  covalent geometry    : bond        0.00344 ( 5961)
  covalent geometry    : angle       0.75230 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6887 (mp0)
REVERT: A  330 LYS cc_start: 0.7752 (tttm) cc_final: 0.7377 (tttp)
REVERT: A  347 ASP cc_start: 0.6450 (m-30) cc_final: 0.6003 (m-30)
REVERT: A  363 GLU cc_start: 0.6775 (tp30) cc_final: 0.6012 (tp30)
REVERT: A  525 MET cc_start: 0.5074 (OUTLIER) cc_final: 0.4173 (mpt)
REVERT: A  575 ASP cc_start: 0.7531 (m-30) cc_final: 0.7203 (m-30)
REVERT: A  613 LYS cc_start: 0.8530 (mttt) cc_final: 0.8167 (mmmt)
REVERT: B    8 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8960 (mtmm)
REVERT: B   27 ARG cc_start: 0.9318 (mmp80) cc_final: 0.8961 (mmp80)
  outliers start: 23
  outliers final: 9
  residues processed: 86
  average time/residue: 0.7494
  time to fit residues: 69.4031
Evaluate side-chains
  67 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    0.0060
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.144456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.118211 restraints weight = 14411.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 5.46
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5979  Z= 0.122
  Angle     :  0.750   9.530   8135  Z= 0.347
  Chirality :  0.050   0.601    976
  Planarity :  0.004   0.048   1014
  Dihedral  :  7.042  54.040   1032
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.47 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 21.51 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.31), residues: 697
  helix: -0.39 (0.60), residues: 69
  sheet: -3.95 (0.49), residues: 75
  loop : -1.92 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 452 
 HIS   0.002   0.000   HIS A 108 
 PHE   0.023   0.001   PHE A 119 
 TYR   0.025   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00728 (   10)
  link_NAG-ASN         : angle       2.33226 (   30)
  link_BETA1-4         : bond        0.00447 (    4)
  link_BETA1-4         : angle       1.84207 (   12)
  hydrogen bonds       : bond        0.04690 (   69)
  hydrogen bonds       : angle       5.33386 (  162)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       1.14860 (    8)
  covalent geometry    : bond        0.00280 ( 5961)
  covalent geometry    : angle       0.73488 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 64
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A  330 LYS cc_start: 0.7669 (tttm) cc_final: 0.7328 (ttmp)
REVERT: A  347 ASP cc_start: 0.6465 (m-30) cc_final: 0.5997 (m-30)
REVERT: A  361 ASN cc_start: 0.7175 (OUTLIER) cc_final: 0.6743 (t0)
REVERT: A  525 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4276 (mpt)
REVERT: A  575 ASP cc_start: 0.7548 (m-30) cc_final: 0.7188 (m-30)
REVERT: B   12 ARG cc_start: 0.8525 (ptt180) cc_final: 0.8051 (ptm160)
REVERT: B   15 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8678 (mm-30)
REVERT: B   27 ARG cc_start: 0.9308 (mmp80) cc_final: 0.8959 (mmp80)
  outliers start: 26
  outliers final: 11
  residues processed: 84
  average time/residue: 0.7128
  time to fit residues: 64.7900
Evaluate side-chains
  73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   chunk 67 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0010
   overall best weight:    0.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.143380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.117298 restraints weight = 14479.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.4353 rms_B_bonded: 5.43
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5979  Z= 0.131
  Angle     :  0.769  10.832   8135  Z= 0.352
  Chirality :  0.049   0.570    976
  Planarity :  0.004   0.048   1014
  Dihedral  :  6.817  54.084   1032
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.76 %
    Favored  : 89.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.12 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.31), residues: 697
  helix: -0.38 (0.59), residues: 69
  sheet: -3.79 (0.51), residues: 75
  loop : -1.90 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 452 
 HIS   0.004   0.000   HIS A 359 
 PHE   0.009   0.001   PHE A  71 
 TYR   0.028   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (   10)
  link_NAG-ASN         : angle       2.45102 (   30)
  link_BETA1-4         : bond        0.00386 (    4)
  link_BETA1-4         : angle       1.72513 (   12)
  hydrogen bonds       : bond        0.04630 (   69)
  hydrogen bonds       : angle       5.28458 (  162)
  SS BOND              : bond        0.00298 (    4)
  SS BOND              : angle       0.96521 (    8)
  covalent geometry    : bond        0.00303 ( 5961)
  covalent geometry    : angle       0.75331 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  330 LYS cc_start: 0.7669 (tttm) cc_final: 0.7241 (tppt)
REVERT: A  347 ASP cc_start: 0.6531 (m-30) cc_final: 0.6057 (m-30)
REVERT: A  361 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6357 (t0)
REVERT: A  363 GLU cc_start: 0.6833 (tp30) cc_final: 0.5841 (tp30)
REVERT: A  525 MET cc_start: 0.5264 (OUTLIER) cc_final: 0.4354 (mpt)
REVERT: A  575 ASP cc_start: 0.7553 (m-30) cc_final: 0.7206 (m-30)
REVERT: B    5 TYR cc_start: 0.8387 (t80) cc_final: 0.8185 (t80)
REVERT: B   12 ARG cc_start: 0.8582 (ptt180) cc_final: 0.8076 (ptm160)
REVERT: B   27 ARG cc_start: 0.9302 (mmp80) cc_final: 0.8974 (mmp80)
  outliers start: 19
  outliers final: 11
  residues processed: 80
  average time/residue: 0.7491
  time to fit residues: 64.6759
Evaluate side-chains
  74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0970
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.143857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.117748 restraints weight = 14303.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4366 rms_B_bonded: 5.39
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.4229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5979  Z= 0.121
  Angle     :  0.766   9.958   8135  Z= 0.349
  Chirality :  0.050   0.662    976
  Planarity :  0.004   0.047   1014
  Dihedral  :  6.575  54.115   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 24.27 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.31), residues: 697
  helix: -0.68 (0.55), residues: 76
  sheet: -3.63 (0.54), residues: 70
  loop : -1.99 (0.26), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 452 
 HIS   0.002   0.000   HIS A 108 
 PHE   0.025   0.001   PHE A 119 
 TYR   0.028   0.002   TYR B   6 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00789 (   10)
  link_NAG-ASN         : angle       2.49905 (   30)
  link_BETA1-4         : bond        0.00485 (    4)
  link_BETA1-4         : angle       1.66105 (   12)
  hydrogen bonds       : bond        0.04650 (   69)
  hydrogen bonds       : angle       5.19457 (  162)
  SS BOND              : bond        0.00263 (    4)
  SS BOND              : angle       0.80863 (    8)
  covalent geometry    : bond        0.00275 ( 5961)
  covalent geometry    : angle       0.74982 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLU cc_start: 0.7727 (mp0) cc_final: 0.7479 (mp0)
REVERT: A  330 LYS cc_start: 0.7656 (tttm) cc_final: 0.7257 (tppt)
REVERT: A  347 ASP cc_start: 0.6574 (m-30) cc_final: 0.6090 (m-30)
REVERT: A  525 MET cc_start: 0.5319 (OUTLIER) cc_final: 0.4408 (mpt)
REVERT: A  575 ASP cc_start: 0.7556 (m-30) cc_final: 0.7242 (m-30)
REVERT: B    8 LYS cc_start: 0.9227 (pttp) cc_final: 0.9023 (pttp)
REVERT: B   27 ARG cc_start: 0.9289 (mmp80) cc_final: 0.8933 (mmp80)
  outliers start: 23
  outliers final: 11
  residues processed: 85
  average time/residue: 0.7582
  time to fit residues: 69.7618
Evaluate side-chains
  74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain B residue   35 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.139559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.112721 restraints weight = 14622.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.4277 rms_B_bonded: 5.43
r_work (final): 0.4277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6819
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5979  Z= 0.207
  Angle     :  0.837  13.097   8135  Z= 0.391
  Chirality :  0.054   0.781    976
  Planarity :  0.004   0.049   1014
  Dihedral  :  6.654  54.193   1032
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.48 %
    Favored  : 87.37 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.04 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.31), residues: 697
  helix: -0.66 (0.56), residues: 75
  sheet: -3.73 (0.53), residues: 75
  loop : -1.98 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 452 
 HIS   0.004   0.001   HIS A 108 
 PHE   0.015   0.002   PHE A 294 
 TYR   0.031   0.003   TYR B   6 
 ARG   0.004   0.000   ARG B  12 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00898 (   10)
  link_NAG-ASN         : angle       2.89321 (   30)
  link_BETA1-4         : bond        0.00336 (    4)
  link_BETA1-4         : angle       1.63378 (   12)
  hydrogen bonds       : bond        0.05605 (   69)
  hydrogen bonds       : angle       5.37047 (  162)
  SS BOND              : bond        0.00391 (    4)
  SS BOND              : angle       1.05287 (    8)
  covalent geometry    : bond        0.00488 ( 5961)
  covalent geometry    : angle       0.81803 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 65
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLU cc_start: 0.7779 (mp0) cc_final: 0.7565 (mp0)
REVERT: A  330 LYS cc_start: 0.7713 (tttm) cc_final: 0.7270 (tppt)
REVERT: A  347 ASP cc_start: 0.6777 (m-30) cc_final: 0.6369 (m-30)
REVERT: A  525 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.4457 (mpt)
REVERT: A  575 ASP cc_start: 0.7642 (m-30) cc_final: 0.7384 (m-30)
REVERT: B    8 LYS cc_start: 0.9242 (pttp) cc_final: 0.9031 (pttp)
REVERT: B   19 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8418 (OUTLIER)
REVERT: B   27 ARG cc_start: 0.9312 (mmp80) cc_final: 0.9021 (mmp80)
  outliers start: 24
  outliers final: 17
  residues processed: 81
  average time/residue: 0.8906
  time to fit residues: 77.5790
Evaluate side-chains
  76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   35 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0060
   chunk 6 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 54 optimal weight:    0.1980
   chunk 44 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.142427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.116356 restraints weight = 14280.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 5.38
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5979  Z= 0.126
  Angle     :  0.802  11.708   8135  Z= 0.366
  Chirality :  0.052   0.745    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.487  53.939   1032
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.50 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (0.31), residues: 697
  helix: -0.55 (0.57), residues: 75
  sheet: -3.59 (0.57), residues: 70
  loop : -1.96 (0.26), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 452 
 HIS   0.002   0.000   HIS A 108 
 PHE   0.027   0.001   PHE A 119 
 TYR   0.031   0.002   TYR B   5 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00887 (   10)
  link_NAG-ASN         : angle       2.68200 (   30)
  link_BETA1-4         : bond        0.00527 (    4)
  link_BETA1-4         : angle       1.54901 (   12)
  hydrogen bonds       : bond        0.04972 (   69)
  hydrogen bonds       : angle       5.24301 (  162)
  SS BOND              : bond        0.00282 (    4)
  SS BOND              : angle       0.75735 (    8)
  covalent geometry    : bond        0.00288 ( 5961)
  covalent geometry    : angle       0.78519 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 LEU cc_start: 0.7010 (tp) cc_final: 0.6803 (tt)
REVERT: A  330 LYS cc_start: 0.7713 (tttm) cc_final: 0.7222 (tppt)
REVERT: A  347 ASP cc_start: 0.6781 (m-30) cc_final: 0.6288 (m-30)
REVERT: A  361 ASN cc_start: 0.6936 (OUTLIER) cc_final: 0.6448 (t0)
REVERT: A  525 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.4589 (mpt)
REVERT: A  575 ASP cc_start: 0.7638 (m-30) cc_final: 0.7331 (m-30)
REVERT: B    8 LYS cc_start: 0.9190 (pttp) cc_final: 0.8974 (pttp)
  outliers start: 22
  outliers final: 13
  residues processed: 79
  average time/residue: 0.6584
  time to fit residues: 56.5914
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.141604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.115360 restraints weight = 14664.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4334 rms_B_bonded: 5.46
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.4696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   5979  Z= 0.144
  Angle     :  0.826  14.155   8135  Z= 0.381
  Chirality :  0.053   0.739    976
  Planarity :  0.004   0.047   1014
  Dihedral  :  6.518  54.139   1032
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.42 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.31), residues: 697
  helix: -0.62 (0.58), residues: 75
  sheet: -3.56 (0.56), residues: 72
  loop : -1.96 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 546 
 HIS   0.003   0.000   HIS A 108 
 PHE   0.013   0.001   PHE A 268 
 TYR   0.024   0.002   TYR B   5 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00829 (   10)
  link_NAG-ASN         : angle       3.58571 (   30)
  link_BETA1-4         : bond        0.00382 (    4)
  link_BETA1-4         : angle       1.47458 (   12)
  hydrogen bonds       : bond        0.05322 (   69)
  hydrogen bonds       : angle       5.32453 (  162)
  SS BOND              : bond        0.00303 (    4)
  SS BOND              : angle       0.79140 (    8)
  covalent geometry    : bond        0.00342 ( 5961)
  covalent geometry    : angle       0.79678 ( 8085)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 LYS cc_start: 0.7692 (tttm) cc_final: 0.7218 (tppt)
REVERT: A  347 ASP cc_start: 0.6821 (m-30) cc_final: 0.6381 (m-30)
REVERT: A  361 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6691 (t0)
REVERT: A  525 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.4734 (mpt)
REVERT: A  575 ASP cc_start: 0.7648 (m-30) cc_final: 0.7351 (m-30)
REVERT: B    4 GLU cc_start: 0.8753 (mp0) cc_final: 0.8514 (mp0)
REVERT: B    8 LYS cc_start: 0.9182 (pttp) cc_final: 0.8811 (pttm)
REVERT: B   19 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8360 (OUTLIER)
  outliers start: 18
  outliers final: 13
  residues processed: 71
  average time/residue: 0.7796
  time to fit residues: 59.7420
Evaluate side-chains
  67 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  615 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.141894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.115721 restraints weight = 14763.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 5.56
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5979  Z= 0.136
  Angle     :  0.818  15.381   8135  Z= 0.374
  Chirality :  0.051   0.646    976
  Planarity :  0.004   0.047   1014
  Dihedral  :  6.370  54.142   1032
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 25.96 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.31), residues: 697
  helix: -0.66 (0.58), residues: 75
  sheet: -3.85 (0.55), residues: 64
  loop : -1.99 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 546 
 HIS   0.003   0.000   HIS A 359 
 PHE   0.025   0.001   PHE A 119 
 TYR   0.025   0.002   TYR B   5 
 ARG   0.003   0.000   ARG A 394 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00870 (   10)
  link_NAG-ASN         : angle       3.70084 (   30)
  link_BETA1-4         : bond        0.00447 (    4)
  link_BETA1-4         : angle       1.37992 (   12)
  hydrogen bonds       : bond        0.05041 (   69)
  hydrogen bonds       : angle       5.37405 (  162)
  SS BOND              : bond        0.00283 (    4)
  SS BOND              : angle       0.74976 (    8)
  covalent geometry    : bond        0.00321 ( 5961)
  covalent geometry    : angle       0.78671 ( 8085)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4184.89 seconds
wall clock time: 73 minutes 39.17 seconds (4419.17 seconds total)