Starting phenix.real_space_refine
on Wed Jun  4 14:58:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gh6_51348/06_2025/9gh6_51348_trim.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    1033      2.51       5
     N     273      2.21       5
     O     352      1.98       5
     H    1498      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3159
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 3061
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 3061
          Classifications: {'peptide': 200}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 184}
    Chain: "D"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 98
          Unusual residues: {'NAG': 7}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
  Time building chain proxies: 2.46, per 1000 atoms: 0.78
  Number of scatterers: 3159
  At special positions: 0
  Unit cell: (93.79, 62.25, 51.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       3     16.00
     O     352      8.00
     N     273      7.00
     C    1033      6.00
     H    1498      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 167 " - pdb=" SG  CYS D 215 " 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
    NAG-ASN
      " NAG D 501 " - " ASN D 104 "
      " NAG D 502 " - " ASN D 111 "
      " NAG D 503 " - " ASN D 182 "
      " NAG D 504 " - " ASN D 197 "
      " NAG D 505 " - " ASN D 152 "
      " NAG D 506 " - " ASN D 224 "
      " NAG D 507 " - " ASN D 208 "
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 209.7 milliseconds
  

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  376

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 4 sheets defined
      6.5% alpha, 36.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'D' and resid 74 through 76
      No H-bonds generated for 'chain 'D' and resid 74 through 76'
    Processing helix  chain 'D' and resid 113 through 117
    Processing helix  chain 'D' and resid 206 through 210
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 41
    Processing sheet with id=AA2, first strand: chain 'D' and resid 44 through 46
      removed outlier: 6.269A  pdb=" N   VAL D  45 " --> pdb=" O   TYR D 141 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE D 138 " --> pdb=" O   GLY D 118 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY D 118 " --> pdb=" O   PHE D 138 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   PHE D 119 " --> pdb=" O   LYS D  69 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   LYS D  69 " --> pdb=" O   PHE D 119 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   THR D 121 " --> pdb=" O   TRP D  67 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   TRP D  67 " --> pdb=" O   THR D 121 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLN D 123 " --> pdb=" O   TYR D  65 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   TYR D  65 " --> pdb=" O   GLN D 123 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE D 125 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 8.203A  pdb=" N   PHE D  63 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   ALA D  83 " --> pdb=" O   PHE D  63 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   TYR D  65 " --> pdb=" O   GLY D  81 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   GLY D  81 " --> pdb=" O   TYR D  65 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   TRP D  67 " --> pdb=" O   ILE D  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 149 through 151
    Processing sheet with id=AA4, first strand: chain 'D' and resid 183 through 184
      removed outlier: 3.782A  pdb=" N   ILE D 217 " --> pdb=" O   ASN D 224 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASN D 224 " --> pdb=" O   ILE D 217 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    99 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1498
        1.03 -     1.23: 14
        1.23 -     1.43: 666
        1.43 -     1.62: 1012
        1.62 -     1.82: 4
  Bond restraints: 3194
  Sorted by residual:
  bond pdb=" C7  NAG D 503 "
       pdb=" N2  NAG D 503 "
    ideal  model  delta    sigma   weight residual
    1.346  1.465 -0.119 2.00e-02 2.50e+03 3.52e+01
  bond pdb=" C7  NAG D 506 "
       pdb=" N2  NAG D 506 "
    ideal  model  delta    sigma   weight residual
    1.346  1.464 -0.118 2.00e-02 2.50e+03 3.50e+01
  bond pdb=" C7  NAG D 504 "
       pdb=" N2  NAG D 504 "
    ideal  model  delta    sigma   weight residual
    1.346  1.464 -0.118 2.00e-02 2.50e+03 3.49e+01
  bond pdb=" C7  NAG D 505 "
       pdb=" N2  NAG D 505 "
    ideal  model  delta    sigma   weight residual
    1.346  1.464 -0.118 2.00e-02 2.50e+03 3.48e+01
  bond pdb=" C7  NAG D 507 "
       pdb=" N2  NAG D 507 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.44e+01
  ... (remaining 3189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 5312
        1.14 -     2.27: 310
        2.27 -     3.41: 60
        3.41 -     4.55: 19
        4.55 -     5.69: 21
  Bond angle restraints: 5722
  Sorted by residual:
  angle pdb=" N   GLY D 196 "
        pdb=" CA  GLY D 196 "
        pdb=" C   GLY D 196 "
      ideal   model   delta    sigma   weight residual
     113.18  107.49    5.69 2.37e+00 1.78e-01 5.75e+00
  angle pdb=" N   ASN D 219 "
        pdb=" CA  ASN D 219 "
        pdb=" C   ASN D 219 "
      ideal   model   delta    sigma   weight residual
     110.58  107.25    3.33 1.56e+00 4.11e-01 4.56e+00
  angle pdb=" C3  NAG D 506 "
        pdb=" C4  NAG D 506 "
        pdb=" C5  NAG D 506 "
      ideal   model   delta    sigma   weight residual
     109.38  114.94   -5.56 3.00e+00 1.11e-01 3.44e+00
  angle pdb=" C1  NAG D 506 "
        pdb=" O5  NAG D 506 "
        pdb=" C5  NAG D 506 "
      ideal   model   delta    sigma   weight residual
     113.21  107.77    5.44 3.00e+00 1.11e-01 3.28e+00
  angle pdb=" C2  NAG D 506 "
        pdb=" C3  NAG D 506 "
        pdb=" C4  NAG D 506 "
      ideal   model   delta    sigma   weight residual
     110.24  115.58   -5.34 3.00e+00 1.11e-01 3.17e+00
  ... (remaining 5717 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 1448
       17.64 -    35.28: 134
       35.28 -    52.92: 28
       52.92 -    70.56: 17
       70.56 -    88.19: 4
  Dihedral angle restraints: 1631
    sinusoidal: 967
      harmonic: 664
  Sorted by residual:
  dihedral pdb=" CA  ASN D 224 "
           pdb=" C   ASN D 224 "
           pdb=" N   ARG D 225 "
           pdb=" CA  ARG D 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.52  -20.48     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASN D 195 "
           pdb=" C   ASN D 195 "
           pdb=" N   GLY D 196 "
           pdb=" CA  GLY D 196 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.23  -18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLY D 196 "
           pdb=" C   GLY D 196 "
           pdb=" N   ASN D 197 "
           pdb=" CA  ASN D 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.86   18.14     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 1628 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 232
       0.064 -    0.128: 42
       0.128 -    0.192: 10
       0.192 -    0.257: 0
       0.257 -    0.321: 1
  Chirality restraints: 285
  Sorted by residual:
  chirality pdb=" C1  NAG D 506 "
            pdb=" ND2 ASN D 224 "
            pdb=" C2  NAG D 506 "
            pdb=" O5  NAG D 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" C5  NAG D 503 "
            pdb=" C4  NAG D 503 "
            pdb=" C6  NAG D 503 "
            pdb=" O5  NAG D 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.59    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" C5  NAG D 501 "
            pdb=" C4  NAG D 501 "
            pdb=" C6  NAG D 501 "
            pdb=" O5  NAG D 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.59    0.18 2.00e-01 2.50e+01 7.81e-01
  ... (remaining 282 not shown)

  Planarity restraints: 491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 219 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO D 220 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO D 220 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO D 220 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU D 168 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO D 169 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO D 169 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 169 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 144 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO D 145 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO D 145 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO D 145 "    0.015 5.00e-02 4.00e+02
  ... (remaining 488 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 205
        2.20 -     2.80: 6245
        2.80 -     3.40: 8194
        3.40 -     4.00: 10935
        4.00 -     4.60: 16147
  Nonbonded interactions: 41726
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 170 "
            pdb=" HH  TYR D 176 "
     model   vdw
     1.596 2.450
  nonbonded pdb=" H   LYS D 146 "
            pdb=" O6  NAG D 506 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" H   THR D 206 "
            pdb=" OD2 ASP D 209 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OD1 ASN D 219 "
            pdb=" H   SER D 222 "
     model   vdw
     1.641 2.450
  nonbonded pdb=" OE1 GLU D 216 "
            pdb=" HE  ARG D 225 "
     model   vdw
     1.646 2.450
  ... (remaining 41721 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.330
  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:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.060
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:14.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6596
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      :  0.014   0.119   1704  Z= 0.705
  Angle     :  0.906   5.685   2346  Z= 0.389
  Chirality :  0.058   0.321    285
  Planarity :  0.004   0.031    300
  Dihedral  : 13.765  88.194    734
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.20 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.22 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.56 (0.55), residues: 97
  loop : -0.18 (0.65), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D 178 
 HIS   0.000   0.000   HIS D  56 
 PHE   0.002   0.000   PHE D  43 
 TYR   0.005   0.001   TYR D  82 
 ARG   0.004   0.001   ARG D  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    7)
  link_NAG-ASN         : angle       2.04223 (   21)
  hydrogen bonds       : bond        0.23318 (   44)
  hydrogen bonds       : angle       8.60703 (   99)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       0.98220 (    2)
  covalent geometry    : bond        0.01412 ( 1696)
  covalent geometry    : angle       0.88928 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7349 (mm-40)
REVERT: D   62 LEU cc_start: 0.8108 (mt) cc_final: 0.7753 (mm)
REVERT: D   99 GLU cc_start: 0.6406 (mp0) cc_final: 0.6055 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 73
  average time/residue: 1.2513
  time to fit residues: 93.7921
Evaluate side-chains
  62 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  173 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D  57 ASN
D 123 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.134799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.114144 restraints weight = 7621.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 3.17
r_work: 0.3528 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1704  Z= 0.159
  Angle     :  0.655   5.671   2346  Z= 0.318
  Chirality :  0.050   0.332    285
  Planarity :  0.004   0.032    300
  Dihedral  :  6.116  46.568    365
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.79 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.28 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.76 (0.59), residues: 86
  loop : -0.23 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.007   0.001   PHE D 138 
 TYR   0.009   0.001   TYR D  82 
 ARG   0.002   0.000   ARG D  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00517 (    7)
  link_NAG-ASN         : angle       2.32707 (   21)
  hydrogen bonds       : bond        0.03866 (   44)
  hydrogen bonds       : angle       6.25939 (   99)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.43782 (    2)
  covalent geometry    : bond        0.00364 ( 1696)
  covalent geometry    : angle       0.61965 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7622 (mm-40)
REVERT: D   62 LEU cc_start: 0.8782 (mt) cc_final: 0.8526 (mm)
REVERT: D   96 SER cc_start: 0.8276 (t) cc_final: 0.7988 (p)
REVERT: D   99 GLU cc_start: 0.7597 (mp0) cc_final: 0.7054 (mp0)
REVERT: D  117 THR cc_start: 0.8022 (t) cc_final: 0.7522 (p)
REVERT: D  132 GLU cc_start: 0.7958 (tt0) cc_final: 0.7685 (mt-10)
REVERT: D  133 GLU cc_start: 0.7501 (mp0) cc_final: 0.7293 (mp0)
REVERT: D  178 TRP cc_start: 0.7173 (m100) cc_final: 0.6508 (m100)
REVERT: D  217 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7909 (pp)
REVERT: D  225 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7406 (mtt180)
  outliers start: 6
  outliers final: 2
  residues processed: 65
  average time/residue: 1.3970
  time to fit residues: 93.0285
Evaluate side-chains
  64 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  217 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3907 r_free = 0.3907 target = 0.136625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.115902 restraints weight = 7488.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 3.01
r_work: 0.3546 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1704  Z= 0.154
  Angle     :  0.649   5.874   2346  Z= 0.313
  Chirality :  0.051   0.351    285
  Planarity :  0.004   0.034    300
  Dihedral  :  5.394  45.384    363
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 23.46 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.05 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.44 (0.56), residues: 86
  loop : -0.22 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.008   0.001   PHE D 138 
 TYR   0.014   0.002   TYR D 176 
 ARG   0.001   0.000   ARG D  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00402 (    7)
  link_NAG-ASN         : angle       2.20798 (   21)
  hydrogen bonds       : bond        0.03621 (   44)
  hydrogen bonds       : angle       5.70615 (   99)
  SS BOND              : bond        0.00476 (    1)
  SS BOND              : angle       0.56707 (    2)
  covalent geometry    : bond        0.00357 ( 1696)
  covalent geometry    : angle       0.61696 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7528 (mm-40)
REVERT: D   62 LEU cc_start: 0.8831 (mt) cc_final: 0.8584 (mm)
REVERT: D   99 GLU cc_start: 0.7517 (mp0) cc_final: 0.7076 (mp0)
REVERT: D  132 GLU cc_start: 0.7912 (tt0) cc_final: 0.7659 (mt-10)
  outliers start: 6
  outliers final: 6
  residues processed: 67
  average time/residue: 1.5041
  time to fit residues: 103.0808
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  135 THR
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  217 ILE
Chi-restraints excluded: chain D residue  222 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.116716 restraints weight = 7427.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.97
r_work: 0.3466 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   1704  Z= 0.153
  Angle     :  0.628   6.007   2346  Z= 0.305
  Chirality :  0.051   0.347    285
  Planarity :  0.004   0.035    300
  Dihedral  :  5.406  45.244    363
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 23.46 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.03 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.36 (0.56), residues: 86
  loop : -0.26 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.007   0.001   PHE D 138 
 TYR   0.010   0.002   TYR D 176 
 ARG   0.001   0.000   ARG D  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00382 (    7)
  link_NAG-ASN         : angle       2.14295 (   21)
  hydrogen bonds       : bond        0.03290 (   44)
  hydrogen bonds       : angle       5.53811 (   99)
  SS BOND              : bond        0.00260 (    1)
  SS BOND              : angle       0.57005 (    2)
  covalent geometry    : bond        0.00362 ( 1696)
  covalent geometry    : angle       0.59721 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7649 (mm-40)
REVERT: D   62 LEU cc_start: 0.8943 (mt) cc_final: 0.8654 (mm)
REVERT: D   99 GLU cc_start: 0.7711 (mp0) cc_final: 0.7257 (mp0)
REVERT: D  132 GLU cc_start: 0.8122 (tt0) cc_final: 0.7876 (mt-10)
REVERT: D  229 VAL cc_start: 0.8744 (t) cc_final: 0.8274 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 1.4696
  time to fit residues: 102.2959
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  135 THR
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  217 ILE
Chi-restraints excluded: chain D residue  222 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3895 r_free = 0.3895 target = 0.135517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.115206 restraints weight = 7475.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 3.02
r_work: 0.3535 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1704  Z= 0.155
  Angle     :  0.629   6.099   2346  Z= 0.308
  Chirality :  0.051   0.349    285
  Planarity :  0.004   0.033    300
  Dihedral  :  5.472  45.016    363
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 25.70 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.26 (0.56), residues: 85
  loop : -0.22 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 179 
 HIS   0.003   0.002   HIS D 139 
 PHE   0.006   0.001   PHE D 138 
 TYR   0.007   0.001   TYR D 176 
 ARG   0.001   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00370 (    7)
  link_NAG-ASN         : angle       2.17046 (   21)
  hydrogen bonds       : bond        0.03273 (   44)
  hydrogen bonds       : angle       5.37737 (   99)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       0.63633 (    2)
  covalent geometry    : bond        0.00358 ( 1696)
  covalent geometry    : angle       0.59721 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7541 (mm-40)
REVERT: D   62 LEU cc_start: 0.8897 (mt) cc_final: 0.8646 (mm)
REVERT: D   99 GLU cc_start: 0.7468 (mp0) cc_final: 0.7193 (mp0)
REVERT: D  132 GLU cc_start: 0.7935 (tt0) cc_final: 0.7725 (mt-10)
REVERT: D  216 GLU cc_start: 0.6829 (tt0) cc_final: 0.6077 (tt0)
REVERT: D  229 VAL cc_start: 0.8759 (t) cc_final: 0.8296 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 70
  average time/residue: 1.4225
  time to fit residues: 101.9919
Evaluate side-chains
  69 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  135 THR
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0470
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3890 r_free = 0.3890 target = 0.135549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.114767 restraints weight = 7552.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 3.13
r_work: 0.3490 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   1704  Z= 0.128
  Angle     :  0.616   5.769   2346  Z= 0.302
  Chirality :  0.051   0.345    285
  Planarity :  0.005   0.048    300
  Dihedral  :  5.543  44.252    363
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 26.26 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.19 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.30 (0.55), residues: 86
  loop : -0.41 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 179 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.004   0.001   PHE D 138 
 TYR   0.011   0.001   TYR D 176 
 ARG   0.001   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00365 (    7)
  link_NAG-ASN         : angle       2.04688 (   21)
  hydrogen bonds       : bond        0.03081 (   44)
  hydrogen bonds       : angle       5.24200 (   99)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       1.31946 (    2)
  covalent geometry    : bond        0.00307 ( 1696)
  covalent geometry    : angle       0.58688 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7551 (mm-40)
REVERT: D   62 LEU cc_start: 0.8881 (mt) cc_final: 0.8617 (mm)
REVERT: D   99 GLU cc_start: 0.7492 (mp0) cc_final: 0.7201 (mp0)
REVERT: D  132 GLU cc_start: 0.7909 (tt0) cc_final: 0.7697 (mt-10)
REVERT: D  216 GLU cc_start: 0.6908 (tt0) cc_final: 0.6042 (tt0)
REVERT: D  225 ARG cc_start: 0.7559 (mtt180) cc_final: 0.6458 (mtt180)
REVERT: D  229 VAL cc_start: 0.8777 (t) cc_final: 0.8313 (m)
  outliers start: 6
  outliers final: 6
  residues processed: 65
  average time/residue: 1.4975
  time to fit residues: 99.5554
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  218 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3894 r_free = 0.3894 target = 0.135884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.115503 restraints weight = 7408.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 3.08
r_work: 0.3503 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1704  Z= 0.165
  Angle     :  0.627   6.083   2346  Z= 0.309
  Chirality :  0.051   0.342    285
  Planarity :  0.005   0.047    300
  Dihedral  :  5.787  45.250    363
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.37 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.29 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.14 (0.55), residues: 85
  loop : -0.38 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 179 
 HIS   0.003   0.002   HIS D  56 
 PHE   0.004   0.001   PHE D 138 
 TYR   0.008   0.002   TYR D 213 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00381 (    7)
  link_NAG-ASN         : angle       2.11971 (   21)
  hydrogen bonds       : bond        0.03196 (   44)
  hydrogen bonds       : angle       5.33738 (   99)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       1.31690 (    2)
  covalent geometry    : bond        0.00384 ( 1696)
  covalent geometry    : angle       0.59599 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7509 (mm-40)
REVERT: D   62 LEU cc_start: 0.8898 (mt) cc_final: 0.8645 (mm)
REVERT: D   99 GLU cc_start: 0.7478 (mp0) cc_final: 0.7181 (mp0)
REVERT: D  216 GLU cc_start: 0.6959 (tt0) cc_final: 0.6115 (tt0)
REVERT: D  225 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6497 (mtt180)
REVERT: D  229 VAL cc_start: 0.8780 (t) cc_final: 0.8328 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 1.4023
  time to fit residues: 96.3796
Evaluate side-chains
  66 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  135 THR
Chi-restraints excluded: chain D residue  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3861 r_free = 0.3861 target = 0.133851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.113027 restraints weight = 7376.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.05
r_work: 0.3463 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   1704  Z= 0.148
  Angle     :  0.622   5.732   2346  Z= 0.310
  Chirality :  0.051   0.330    285
  Planarity :  0.005   0.045    300
  Dihedral  :  6.235  48.213    363
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 28.49 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.40 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet: -0.01 (0.55), residues: 87
  loop : -0.40 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.003   0.001   PHE D  43 
 TYR   0.004   0.001   TYR D 102 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00371 (    7)
  link_NAG-ASN         : angle       2.02891 (   21)
  hydrogen bonds       : bond        0.03084 (   44)
  hydrogen bonds       : angle       5.24525 (   99)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.97039 (    2)
  covalent geometry    : bond        0.00347 ( 1696)
  covalent geometry    : angle       0.59377 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7500 (mm-40)
REVERT: D   62 LEU cc_start: 0.8898 (mt) cc_final: 0.8647 (mm)
REVERT: D   99 GLU cc_start: 0.7500 (mp0) cc_final: 0.7211 (mp0)
REVERT: D  229 VAL cc_start: 0.8745 (t) cc_final: 0.8282 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 62
  average time/residue: 1.5079
  time to fit residues: 95.6493
Evaluate side-chains
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   50 GLU
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3879 r_free = 0.3879 target = 0.135746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115285 restraints weight = 7424.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 3.06
r_work: 0.3531 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.4143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1704  Z= 0.150
  Angle     :  0.635   5.692   2346  Z= 0.314
  Chirality :  0.051   0.319    285
  Planarity :  0.005   0.045    300
  Dihedral  :  6.604  56.237    363
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 29.05 %
    Favored  : 66.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.00 (0.55), residues: 87
  loop : -0.44 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.006   0.001   PHE D 165 
 TYR   0.009   0.001   TYR D 213 
 ARG   0.003   0.001   ARG D 190 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (    7)
  link_NAG-ASN         : angle       2.01101 (   21)
  hydrogen bonds       : bond        0.03011 (   44)
  hydrogen bonds       : angle       5.24485 (   99)
  SS BOND              : bond        0.00185 (    1)
  SS BOND              : angle       1.07472 (    2)
  covalent geometry    : bond        0.00353 ( 1696)
  covalent geometry    : angle       0.60829 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7503 (mm-40)
REVERT: D   62 LEU cc_start: 0.8885 (mt) cc_final: 0.8643 (mm)
REVERT: D   99 GLU cc_start: 0.7480 (mp0) cc_final: 0.7210 (mp0)
REVERT: D  229 VAL cc_start: 0.8720 (t) cc_final: 0.8272 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 63
  average time/residue: 1.5915
  time to fit residues: 102.4670
Evaluate side-chains
  64 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3860 r_free = 0.3860 target = 0.134705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.114069 restraints weight = 7298.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.03
r_work: 0.3447 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1704  Z= 0.139
  Angle     :  0.636   5.584   2346  Z= 0.315
  Chirality :  0.050   0.316    285
  Planarity :  0.005   0.044    300
  Dihedral  :  6.677  57.890    363
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 27.93 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.38 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.08 (0.55), residues: 87
  loop : -0.45 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D  56 
 PHE   0.005   0.001   PHE D 165 
 TYR   0.006   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00339 (    7)
  link_NAG-ASN         : angle       2.00994 (   21)
  hydrogen bonds       : bond        0.03052 (   44)
  hydrogen bonds       : angle       5.15543 (   99)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       1.15767 (    2)
  covalent geometry    : bond        0.00330 ( 1696)
  covalent geometry    : angle       0.60855 ( 2323)

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

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

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  396 Ramachandran restraints generated.
    198 Oldfield, 0 Emsley, 198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7471 (mm-40)
REVERT: D   62 LEU cc_start: 0.8891 (mt) cc_final: 0.8606 (mm)
REVERT: D   99 GLU cc_start: 0.7471 (mp0) cc_final: 0.7138 (mp0)
REVERT: D  153 ASN cc_start: 0.8040 (t0) cc_final: 0.7836 (t0)
REVERT: D  229 VAL cc_start: 0.8660 (t) cc_final: 0.8205 (m)
  outliers start: 7
  outliers final: 7
  residues processed: 63
  average time/residue: 1.6104
  time to fit residues: 103.6901
Evaluate side-chains
  65 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 THR
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  168 GLU
Chi-restraints excluded: chain D residue  197 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 123 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 = 0.3867 r_free = 0.3867 target = 0.134977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.113832 restraints weight = 7330.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 3.07
r_work: 0.3532 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1704  Z= 0.149
  Angle     :  0.647   5.604   2346  Z= 0.323
  Chirality :  0.050   0.301    285
  Planarity :  0.005   0.043    300
  Dihedral  :  6.387  49.739    363
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 29.61 %
    Favored  : 66.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.37 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.11 (0.55), residues: 89
  loop : -0.48 (0.62), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D  56 
 PHE   0.004   0.001   PHE D 165 
 TYR   0.006   0.001   TYR D 176 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00326 (    7)
  link_NAG-ASN         : angle       2.02193 (   21)
  hydrogen bonds       : bond        0.03178 (   44)
  hydrogen bonds       : angle       5.16575 (   99)
  SS BOND              : bond        0.00176 (    1)
  SS BOND              : angle       1.14790 (    2)
  covalent geometry    : bond        0.00348 ( 1696)
  covalent geometry    : angle       0.61972 ( 2323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3959.13 seconds
wall clock time: 67 minutes 47.99 seconds (4067.99 seconds total)