Starting phenix.real_space_refine
on Sat May 10 00:55:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k11_36783/05_2025/8k11_36783.cif"
  }
  resolution = 3.3
  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=   0.062
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      16      5.16       5
     C    2794      2.51       5
     N     716      2.21       5
     O     876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4402
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2089
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 249}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 2089
          Classifications: {'peptide': 263}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 249}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "O"
      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: "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: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.79, per 1000 atoms: 0.86
  Number of scatterers: 4402
  At special positions: 0
  Unit cell: (79.54, 74.62, 67.24, 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      16     16.00
     O     876      8.00
     N     716      7.00
     C    2794      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 256 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 197 " - pdb=" SG  CYS B 256 " 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 O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A 301 " - " ASN A  27 "
      " NAG A 302 " - " ASN A  60 "
      " NAG A 303 " - " ASN A 123 "
      " NAG A 304 " - " ASN A 141 "
      " NAG B 301 " - " ASN B  27 "
      " NAG B 302 " - " ASN B  60 "
      " NAG B 303 " - " ASN B 123 "
      " NAG B 304 " - " ASN B 141 "
      " NAG C   1 " - " ASN B  54 "
      " NAG D   1 " - " ASN A 165 "
      " NAG E   1 " - " ASN B 165 "
      " NAG O   1 " - " ASN A  54 "
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 547.0 milliseconds
  

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1016

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 41.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31
      removed outlier: 3.803A  pdb=" N   VAL A  57 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLU A 126 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.067A  pdb=" N   LYS A 106 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 166
    Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 31
      removed outlier: 3.805A  pdb=" N   VAL B  57 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLU B 126 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 43
    Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100
      removed outlier: 6.069A  pdb=" N   LYS B 106 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 166
    Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 177

    162 hydrogen bonds defined for protein.
    432 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: 1.17

  Time building geometry restraints manager: 1.60 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: 1402
        1.34 -     1.46: 1071
        1.46 -     1.58: 1995
        1.58 -     1.70: 0
        1.70 -     1.82: 24
  Bond restraints: 4492
  Sorted by residual:
  bond pdb=" N   ASN B 214 "
       pdb=" CA  ASN B 214 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.33e-02 5.65e+03 7.43e+00
  bond pdb=" N   ASN A 214 "
       pdb=" CA  ASN A 214 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.33e-02 5.65e+03 7.07e+00
  bond pdb=" N   MET B 221 "
       pdb=" CA  MET B 221 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 1.23e-02 6.61e+03 5.26e+00
  bond pdb=" N   MET A 221 "
       pdb=" CA  MET A 221 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.23e-02 6.61e+03 5.18e+00
  bond pdb=" N   ASP A 204 "
       pdb=" CA  ASP A 204 "
    ideal  model  delta    sigma   weight residual
    1.454  1.482 -0.028 1.34e-02 5.57e+03 4.44e+00
  ... (remaining 4487 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.73: 5259
        0.73 -     1.45: 592
        1.45 -     2.18: 178
        2.18 -     2.90: 63
        2.90 -     3.63: 20
  Bond angle restraints: 6112
  Sorted by residual:
  angle pdb=" CA  PHE B 178 "
        pdb=" CB  PHE B 178 "
        pdb=" CG  PHE B 178 "
      ideal   model   delta    sigma   weight residual
     113.80  116.91   -3.11 1.00e+00 1.00e+00 9.69e+00
  angle pdb=" CA  PHE A 178 "
        pdb=" CB  PHE A 178 "
        pdb=" CG  PHE A 178 "
      ideal   model   delta    sigma   weight residual
     113.80  116.88   -3.08 1.00e+00 1.00e+00 9.47e+00
  angle pdb=" CA  ASP A 204 "
        pdb=" C   ASP A 204 "
        pdb=" O   ASP A 204 "
      ideal   model   delta    sigma   weight residual
     121.87  118.78    3.09 1.16e+00 7.43e-01 7.11e+00
  angle pdb=" CA  ASP B 204 "
        pdb=" C   ASP B 204 "
        pdb=" O   ASP B 204 "
      ideal   model   delta    sigma   weight residual
     121.87  118.87    3.00 1.16e+00 7.43e-01 6.71e+00
  angle pdb=" C   PHE A 178 "
        pdb=" CA  PHE A 178 "
        pdb=" CB  PHE A 178 "
      ideal   model   delta    sigma   weight residual
     109.62  105.99    3.63 1.57e+00 4.06e-01 5.34e+00
  ... (remaining 6107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.74: 2481
       15.74 -    31.49: 320
       31.49 -    47.23: 91
       47.23 -    62.97: 28
       62.97 -    78.71: 6
  Dihedral angle restraints: 2926
    sinusoidal: 1362
      harmonic: 1564
  Sorted by residual:
  dihedral pdb=" CB  CYS A 117 "
           pdb=" SG  CYS A 117 "
           pdb=" SG  CYS A 207 "
           pdb=" CB  CYS A 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.47   36.47     1      1.00e+01 1.00e-02 1.88e+01
  dihedral pdb=" CB  CYS B 117 "
           pdb=" SG  CYS B 117 "
           pdb=" SG  CYS B 207 "
           pdb=" CB  CYS B 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.47   36.47     1      1.00e+01 1.00e-02 1.88e+01
  dihedral pdb=" SG  CYS A 117 "
           pdb=" CB  CYS A 207 "
           pdb=" SG  CYS A 207 "
           pdb=" CA  CYS A 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   18.79   60.21     1      2.00e+01 2.50e-03 1.21e+01
  ... (remaining 2923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 694
       0.104 -    0.207: 48
       0.207 -    0.311: 5
       0.311 -    0.415: 0
       0.415 -    0.519: 1
  Chirality restraints: 748
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 165 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.72e+00
  chirality pdb=" CA  PHE B 178 "
            pdb=" N   PHE B 178 "
            pdb=" C   PHE B 178 "
            pdb=" CB  PHE B 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  PHE A 178 "
            pdb=" N   PHE A 178 "
            pdb=" C   PHE A 178 "
            pdb=" CB  PHE A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.73e+00
  ... (remaining 745 not shown)

  Planarity restraints: 786
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 165 "   -0.039 2.00e-02 2.50e+03   4.81e-02 2.89e+01
        pdb=" CG  ASN B 165 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 165 "    0.082 2.00e-02 2.50e+03
        pdb=" C1  NAG E   1 "   -0.056 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 123 "   -0.038 2.00e-02 2.50e+03   4.19e-02 2.19e+01
        pdb=" CG  ASN B 123 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 123 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 123 "    0.067 2.00e-02 2.50e+03
        pdb=" C1  NAG B 303 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  54 "   -0.019 2.00e-02 2.50e+03   2.13e-02 5.66e+00
        pdb=" CG  ASN B  54 "    0.006 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  54 "    0.006 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  54 "    0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 783 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 480
        2.75 -     3.29: 3887
        3.29 -     3.83: 6736
        3.83 -     4.36: 7686
        4.36 -     4.90: 13590
  Nonbonded interactions: 32379
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 165 "
            pdb=" OG1 THR A 279 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD1 ASN B 165 "
            pdb=" OG1 THR B 279 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU B 116 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   LEU A 116 "
            pdb=" OH  TYR A 173 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ALA B 194 "
            pdb=" OG1 THR B 226 "
     model   vdw
     2.297 3.040
  ... (remaining 32374 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'O'
}

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:             1.910
  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:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.860
  Find NCS groups from input model:        0.170
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
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   4512  Z= 0.227
  Angle     :  0.716  17.163   6168  Z= 0.344
  Chirality :  0.057   0.519    748
  Planarity :  0.003   0.034    774
  Dihedral  : 15.604  78.712   1898
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 23.52 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.68 (0.29), residues: 270
  loop : -1.68 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A  55 
 PHE   0.015   0.001   PHE A 178 
 TYR   0.012   0.001   TYR A 173 
 ARG   0.003   0.000   ARG A 147 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00673 (   12)
  link_NAG-ASN         : angle       5.26205 (   36)
  link_BETA1-4         : bond        0.00388 (    4)
  link_BETA1-4         : angle       1.07754 (   12)
  hydrogen bonds       : bond        0.07132 (  162)
  hydrogen bonds       : angle       5.97429 (  432)
  SS BOND              : bond        0.00282 (    4)
  SS BOND              : angle       0.76991 (    8)
  covalent geometry    : bond        0.00433 ( 4492)
  covalent geometry    : angle       0.59300 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6385 (mtp180)
REVERT: A  112 VAL cc_start: 0.8849 (p) cc_final: 0.8556 (m)
REVERT: B  105 ARG cc_start: 0.6671 (mmm160) cc_final: 0.6376 (mtp180)
REVERT: B  112 VAL cc_start: 0.8856 (p) cc_final: 0.8570 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2189
  time to fit residues: 28.5172
Evaluate side-chains
  64 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 161 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.203431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.158345 restraints weight = 4910.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 3.03
r_work: 0.3624 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4512  Z= 0.117
  Angle     :  0.596   9.277   6168  Z= 0.298
  Chirality :  0.049   0.205    748
  Planarity :  0.003   0.023    774
  Dihedral  :  7.093  58.589    910
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 22.88 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.35), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.91 (0.29), residues: 250
  loop : -1.38 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  55 
 PHE   0.011   0.001   PHE A 243 
 TYR   0.014   0.001   TYR A 176 
 ARG   0.003   0.001   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00586 (   12)
  link_NAG-ASN         : angle       3.37060 (   36)
  link_BETA1-4         : bond        0.00416 (    4)
  link_BETA1-4         : angle       1.04004 (   12)
  hydrogen bonds       : bond        0.03246 (  162)
  hydrogen bonds       : angle       5.40338 (  432)
  SS BOND              : bond        0.00693 (    4)
  SS BOND              : angle       1.09665 (    8)
  covalent geometry    : bond        0.00264 ( 4492)
  covalent geometry    : angle       0.53663 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7554 (mtp85)
REVERT: A  102 MET cc_start: 0.7507 (ttm) cc_final: 0.7170 (ttm)
REVERT: A  112 VAL cc_start: 0.8843 (p) cc_final: 0.8607 (m)
REVERT: A  188 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8633 (mtmm)
REVERT: B   59 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7560 (mtp85)
REVERT: B  102 MET cc_start: 0.7458 (ttm) cc_final: 0.7129 (ttm)
REVERT: B  112 VAL cc_start: 0.8861 (p) cc_final: 0.8594 (m)
REVERT: B  188 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8592 (mtmm)
  outliers start: 18
  outliers final: 8
  residues processed: 71
  average time/residue: 0.2073
  time to fit residues: 18.0370
Evaluate side-chains
  61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  188 LYS
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 18 optimal weight:    0.2980
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 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 = 0.4317 r_free = 0.4317 target = 0.203258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.157155 restraints weight = 4908.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3832 rms_B_bonded: 3.04
r_work: 0.3628 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4512  Z= 0.107
  Angle     :  0.545   8.520   6168  Z= 0.277
  Chirality :  0.048   0.200    748
  Planarity :  0.003   0.023    774
  Dihedral  :  6.226  56.620    910
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 24.36 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.36), residues: 522
  helix: -4.91 (0.41), residues: 14
  sheet:  1.80 (0.29), residues: 258
  loop : -1.18 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  55 
 PHE   0.011   0.001   PHE B 130 
 TYR   0.009   0.001   TYR B 173 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00503 (   12)
  link_NAG-ASN         : angle       2.59847 (   36)
  link_BETA1-4         : bond        0.00290 (    4)
  link_BETA1-4         : angle       1.02263 (   12)
  hydrogen bonds       : bond        0.03168 (  162)
  hydrogen bonds       : angle       5.29299 (  432)
  SS BOND              : bond        0.00958 (    4)
  SS BOND              : angle       1.44141 (    8)
  covalent geometry    : bond        0.00234 ( 4492)
  covalent geometry    : angle       0.50529 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7962 (mtp-110) cc_final: 0.7570 (mtp85)
REVERT: A  102 MET cc_start: 0.7316 (ttm) cc_final: 0.7002 (ttm)
REVERT: A  112 VAL cc_start: 0.8823 (p) cc_final: 0.8574 (m)
REVERT: B   59 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7563 (mtp85)
REVERT: B  112 VAL cc_start: 0.8805 (p) cc_final: 0.8559 (m)
  outliers start: 14
  outliers final: 8
  residues processed: 62
  average time/residue: 0.2260
  time to fit residues: 17.0501
Evaluate side-chains
  60 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 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 = 0.4264 r_free = 0.4264 target = 0.197126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.149290 restraints weight = 4882.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 3.06
r_work: 0.3538 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4512  Z= 0.196
  Angle     :  0.622   8.328   6168  Z= 0.319
  Chirality :  0.051   0.200    748
  Planarity :  0.004   0.025    774
  Dihedral  :  5.451  45.477    910
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.67 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.36), residues: 522
  helix: -4.88 (0.42), residues: 14
  sheet:  1.60 (0.30), residues: 262
  loop : -1.24 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  55 
 PHE   0.020   0.002   PHE A  82 
 TYR   0.016   0.002   TYR B 173 
 ARG   0.006   0.001   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00682 (   12)
  link_NAG-ASN         : angle       2.60324 (   36)
  link_BETA1-4         : bond        0.00302 (    4)
  link_BETA1-4         : angle       0.86405 (   12)
  hydrogen bonds       : bond        0.03728 (  162)
  hydrogen bonds       : angle       5.43340 (  432)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       2.19657 (    8)
  covalent geometry    : bond        0.00474 ( 4492)
  covalent geometry    : angle       0.58539 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A   59 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.7596 (mtp85)
REVERT: A  228 LYS cc_start: 0.6307 (pttm) cc_final: 0.5143 (mtmt)
REVERT: B   59 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7647 (mtp85)
REVERT: B  228 LYS cc_start: 0.6285 (pttm) cc_final: 0.5167 (mtmt)
  outliers start: 19
  outliers final: 13
  residues processed: 72
  average time/residue: 0.1956
  time to fit residues: 17.4676
Evaluate side-chains
  65 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 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 = 0.4280 r_free = 0.4280 target = 0.199207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150606 restraints weight = 4947.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3720 rms_B_bonded: 3.14
r_work: 0.3544 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   4512  Z= 0.149
  Angle     :  0.582   7.880   6168  Z= 0.294
  Chirality :  0.051   0.205    748
  Planarity :  0.003   0.022    774
  Dihedral  :  5.098  39.449    910
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.15 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.65 (0.30), residues: 260
  loop : -1.52 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  55 
 PHE   0.012   0.001   PHE B 130 
 TYR   0.012   0.001   TYR B 173 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00488 (   12)
  link_NAG-ASN         : angle       2.64702 (   36)
  link_BETA1-4         : bond        0.00440 (    4)
  link_BETA1-4         : angle       0.75536 (   12)
  hydrogen bonds       : bond        0.03371 (  162)
  hydrogen bonds       : angle       5.32765 (  432)
  SS BOND              : bond        0.00141 (    4)
  SS BOND              : angle       1.14660 (    8)
  covalent geometry    : bond        0.00353 ( 4492)
  covalent geometry    : angle       0.54584 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7579 (mtp85)
REVERT: A  228 LYS cc_start: 0.6178 (pttm) cc_final: 0.5098 (mtmt)
REVERT: B   59 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7611 (mtp85)
REVERT: B  228 LYS cc_start: 0.6166 (pttm) cc_final: 0.5119 (mtmt)
  outliers start: 15
  outliers final: 12
  residues processed: 58
  average time/residue: 0.2096
  time to fit residues: 15.0845
Evaluate side-chains
  56 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 26 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 GLN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.196469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149846 restraints weight = 4784.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 3.06
r_work: 0.3584 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   4512  Z= 0.124
  Angle     :  0.562   7.550   6168  Z= 0.282
  Chirality :  0.050   0.185    748
  Planarity :  0.003   0.022    774
  Dihedral  :  4.713  33.990    910
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.00 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.69 (0.30), residues: 258
  loop : -1.42 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  55 
 PHE   0.012   0.001   PHE B 130 
 TYR   0.010   0.001   TYR B 173 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (   12)
  link_NAG-ASN         : angle       2.36097 (   36)
  link_BETA1-4         : bond        0.00314 (    4)
  link_BETA1-4         : angle       0.85587 (   12)
  hydrogen bonds       : bond        0.03192 (  162)
  hydrogen bonds       : angle       5.24592 (  432)
  SS BOND              : bond        0.00351 (    4)
  SS BOND              : angle       2.38654 (    8)
  covalent geometry    : bond        0.00287 ( 4492)
  covalent geometry    : angle       0.52657 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7987 (mtp-110) cc_final: 0.7627 (mtp85)
REVERT: A  228 LYS cc_start: 0.6058 (pttm) cc_final: 0.4918 (mtmt)
REVERT: B   59 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7630 (mtp85)
REVERT: B  228 LYS cc_start: 0.6058 (pttm) cc_final: 0.4943 (mtmt)
  outliers start: 13
  outliers final: 13
  residues processed: 55
  average time/residue: 0.1760
  time to fit residues: 12.5168
Evaluate side-chains
  53 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 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 = 0.4257 r_free = 0.4257 target = 0.196001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149267 restraints weight = 4761.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 3.06
r_work: 0.3585 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   4512  Z= 0.133
  Angle     :  0.569   7.369   6168  Z= 0.282
  Chirality :  0.050   0.198    748
  Planarity :  0.003   0.023    774
  Dihedral  :  4.636  33.394    910
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.21 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.62 (0.30), residues: 260
  loop : -1.45 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  55 
 PHE   0.011   0.001   PHE B 130 
 TYR   0.012   0.001   TYR B 173 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00501 (   12)
  link_NAG-ASN         : angle       2.80503 (   36)
  link_BETA1-4         : bond        0.00265 (    4)
  link_BETA1-4         : angle       0.83042 (   12)
  hydrogen bonds       : bond        0.03222 (  162)
  hydrogen bonds       : angle       5.21400 (  432)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       1.32762 (    8)
  covalent geometry    : bond        0.00312 ( 4492)
  covalent geometry    : angle       0.52551 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7964 (mtp-110) cc_final: 0.7612 (mtp85)
REVERT: A  228 LYS cc_start: 0.6189 (pttm) cc_final: 0.4954 (mtmt)
REVERT: B   59 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7674 (mtp85)
REVERT: B  228 LYS cc_start: 0.6183 (pttm) cc_final: 0.4969 (mtmt)
  outliers start: 13
  outliers final: 13
  residues processed: 54
  average time/residue: 0.1770
  time to fit residues: 12.4121
Evaluate side-chains
  51 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.195734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.149245 restraints weight = 4797.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 3.05
r_work: 0.3576 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   4512  Z= 0.127
  Angle     :  0.561   7.141   6168  Z= 0.282
  Chirality :  0.050   0.208    748
  Planarity :  0.003   0.024    774
  Dihedral  :  4.523  32.074    910
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.58 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.63 (0.30), residues: 258
  loop : -1.31 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  55 
 PHE   0.013   0.001   PHE B 130 
 TYR   0.011   0.001   TYR B 173 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00505 (   12)
  link_NAG-ASN         : angle       2.48191 (   36)
  link_BETA1-4         : bond        0.00366 (    4)
  link_BETA1-4         : angle       0.84832 (   12)
  hydrogen bonds       : bond        0.03172 (  162)
  hydrogen bonds       : angle       5.16690 (  432)
  SS BOND              : bond        0.00191 (    4)
  SS BOND              : angle       2.70455 (    8)
  covalent geometry    : bond        0.00297 ( 4492)
  covalent geometry    : angle       0.51974 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7637 (mtp85)
REVERT: A  228 LYS cc_start: 0.6226 (pttm) cc_final: 0.5045 (mtmt)
REVERT: B   59 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7657 (mtp85)
REVERT: B  228 LYS cc_start: 0.6232 (pttm) cc_final: 0.5074 (mtmt)
  outliers start: 16
  outliers final: 15
  residues processed: 51
  average time/residue: 0.1798
  time to fit residues: 11.8543
Evaluate side-chains
  52 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 37
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0970
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0370
   chunk 30 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.5856

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 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 = 0.4286 r_free = 0.4286 target = 0.199956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.152117 restraints weight = 4901.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 3.11
r_work: 0.3576 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   4512  Z= 0.112
  Angle     :  0.543   6.839   6168  Z= 0.273
  Chirality :  0.049   0.195    748
  Planarity :  0.003   0.024    774
  Dihedral  :  4.453  32.644    910
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 25.85 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.62 (0.30), residues: 258
  loop : -1.23 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B  55 
 PHE   0.017   0.001   PHE A  82 
 TYR   0.010   0.001   TYR B 173 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00486 (   12)
  link_NAG-ASN         : angle       2.35815 (   36)
  link_BETA1-4         : bond        0.00312 (    4)
  link_BETA1-4         : angle       0.83977 (   12)
  hydrogen bonds       : bond        0.03107 (  162)
  hydrogen bonds       : angle       5.08616 (  432)
  SS BOND              : bond        0.00433 (    4)
  SS BOND              : angle       2.39884 (    8)
  covalent geometry    : bond        0.00257 ( 4492)
  covalent geometry    : angle       0.50627 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7653 (mtp85)
REVERT: A  228 LYS cc_start: 0.6306 (pttm) cc_final: 0.5186 (mtmt)
REVERT: B   59 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7698 (mtp85)
REVERT: B  228 LYS cc_start: 0.6302 (pttm) cc_final: 0.5211 (mtmt)
  outliers start: 14
  outliers final: 13
  residues processed: 49
  average time/residue: 0.1834
  time to fit residues: 11.5332
Evaluate side-chains
  51 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0770
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 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 = 0.4284 r_free = 0.4284 target = 0.198958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151474 restraints weight = 4851.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 3.17
r_work: 0.3565 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   4512  Z= 0.113
  Angle     :  0.550   7.734   6168  Z= 0.274
  Chirality :  0.049   0.188    748
  Planarity :  0.003   0.024    774
  Dihedral  :  4.394  34.035    910
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.64 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.63 (0.30), residues: 258
  loop : -1.20 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  55 
 PHE   0.014   0.001   PHE A  82 
 TYR   0.010   0.001   TYR A 173 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00474 (   12)
  link_NAG-ASN         : angle       2.28116 (   36)
  link_BETA1-4         : bond        0.00314 (    4)
  link_BETA1-4         : angle       0.86630 (   12)
  hydrogen bonds       : bond        0.03089 (  162)
  hydrogen bonds       : angle       5.00307 (  432)
  SS BOND              : bond        0.00449 (    4)
  SS BOND              : angle       2.15635 (    8)
  covalent geometry    : bond        0.00260 ( 4492)
  covalent geometry    : angle       0.51640 ( 6112)

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

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

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1044 Ramachandran restraints generated.
    522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7682 (mtp85)
REVERT: A  228 LYS cc_start: 0.6312 (pttm) cc_final: 0.5152 (mtmt)
REVERT: B   59 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7714 (mtp85)
REVERT: B  228 LYS cc_start: 0.6311 (pttm) cc_final: 0.5175 (mtmt)
  outliers start: 13
  outliers final: 13
  residues processed: 50
  average time/residue: 0.1942
  time to fit residues: 12.1891
Evaluate side-chains
  52 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  135 SER
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  135 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  190 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 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 = 0.4260 r_free = 0.4260 target = 0.196530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.149759 restraints weight = 4816.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 3.08
r_work: 0.3554 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   4512  Z= 0.120
  Angle     :  0.545   6.487   6168  Z= 0.274
  Chirality :  0.049   0.190    748
  Planarity :  0.003   0.031    774
  Dihedral  :  4.427  34.953    910
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 25.42 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 23.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.36), residues: 522
  helix:  None (None), residues: 0
  sheet:  1.65 (0.30), residues: 258
  loop : -1.15 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  55 
 PHE   0.013   0.001   PHE A  82 
 TYR   0.011   0.001   TYR B 173 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00463 (   12)
  link_NAG-ASN         : angle       2.21339 (   36)
  link_BETA1-4         : bond        0.00273 (    4)
  link_BETA1-4         : angle       0.84914 (   12)
  hydrogen bonds       : bond        0.03136 (  162)
  hydrogen bonds       : angle       4.99820 (  432)
  SS BOND              : bond        0.00368 (    4)
  SS BOND              : angle       2.19220 (    8)
  covalent geometry    : bond        0.00279 ( 4492)
  covalent geometry    : angle       0.51336 ( 6112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2281.39 seconds
wall clock time: 40 minutes 38.72 seconds (2438.72 seconds total)