Starting phenix.real_space_refine
on Fri May  9 17:41:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gh6_51348/05_2025/9gh6_51348_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gh6_51348/05_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_51348/05_2025/9gh6_51348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gh6_51348/05_2025/9gh6_51348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gh6_51348/05_2025/9gh6_51348_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gh6_51348/05_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 2.73, per 1000 atoms: 0.86
  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: 0.85
  Conformation dependent library (CDL) restraints added in 226.7 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: 0.34
  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: 1.04

  Time building geometry restraints manager: 1.03 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:             1.360
  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:                     13.000
  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:11.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.140
-------------------------------------------------------------------------------
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  : 0.218 
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: 1.2185
  time to fit residues: 91.3807
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  : 0.246 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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
D 172 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.134127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.113527 restraints weight = 7576.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 3.15
r_work: 0.3528 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   1704  Z= 0.166
  Angle     :  0.651   5.760   2346  Z= 0.318
  Chirality :  0.050   0.329    285
  Planarity :  0.004   0.032    300
  Dihedral  :  6.092  46.869    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 :  3.91 %
    Allowed  : 21.79 %
    Favored  : 74.30 %
  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:  0.73 (0.59), residues: 86
  loop : -0.21 (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   0.009   0.001   TYR D  82 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00568 (    7)
  link_NAG-ASN         : angle       2.29602 (   21)
  hydrogen bonds       : bond        0.04294 (   44)
  hydrogen bonds       : angle       6.25771 (   99)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       0.45281 (    2)
  covalent geometry    : bond        0.00376 ( 1696)
  covalent geometry    : angle       0.61649 ( 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
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.197 
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: 0.8097 (mm-40) cc_final: 0.7628 (mm-40)
REVERT: D   62 LEU cc_start: 0.8788 (mt) cc_final: 0.8528 (mm)
REVERT: D   96 SER cc_start: 0.8281 (t) cc_final: 0.8001 (p)
REVERT: D   99 GLU cc_start: 0.7590 (mp0) cc_final: 0.7037 (mp0)
REVERT: D  132 GLU cc_start: 0.7962 (tt0) cc_final: 0.7683 (mt-10)
REVERT: D  133 GLU cc_start: 0.7522 (mp0) cc_final: 0.7310 (mp0)
REVERT: D  178 TRP cc_start: 0.7180 (m100) cc_final: 0.6461 (m100)
REVERT: D  200 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7697 (tp)
REVERT: D  217 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7918 (pp)
REVERT: D  225 ARG cc_start: 0.7744 (mtt180) cc_final: 0.7430 (mtt180)
  outliers start: 7
  outliers final: 4
  residues processed: 67
  average time/residue: 1.3493
  time to fit residues: 92.6726
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  : 0.237 
-------------------------------------------------------------------------------
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  200 LEU
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:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.136960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.116374 restraints weight = 7346.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.97
r_work: 0.3545 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1704  Z= 0.159
  Angle     :  0.653   5.843   2346  Z= 0.314
  Chirality :  0.051   0.352    285
  Planarity :  0.004   0.032    300
  Dihedral  :  5.414  45.319    363
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 24.02 %
    Favored  : 72.63 %
  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:  0.09 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.49 (0.56), residues: 86
  loop : -0.23 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.008   0.001   PHE D 138 
 TYR   0.009   0.001   TYR D 176 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00417 (    7)
  link_NAG-ASN         : angle       2.21358 (   21)
  hydrogen bonds       : bond        0.03660 (   44)
  hydrogen bonds       : angle       5.73816 (   99)
  SS BOND              : bond        0.00351 (    1)
  SS BOND              : angle       0.52014 (    2)
  covalent geometry    : bond        0.00372 ( 1696)
  covalent geometry    : angle       0.62123 ( 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  : 0.240 
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: 0.8039 (mm-40) cc_final: 0.7526 (mm-40)
REVERT: D   62 LEU cc_start: 0.8871 (mt) cc_final: 0.8613 (mm)
REVERT: D   99 GLU cc_start: 0.7527 (mp0) cc_final: 0.7079 (mp0)
REVERT: D  132 GLU cc_start: 0.7919 (tt0) cc_final: 0.7662 (mt-10)
REVERT: D  178 TRP cc_start: 0.7304 (m100) cc_final: 0.6466 (m100)
REVERT: D  225 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7492 (mtt180)
  outliers start: 6
  outliers final: 6
  residues processed: 67
  average time/residue: 1.4433
  time to fit residues: 98.9407
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  : 0.255 
-------------------------------------------------------------------------------
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  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  200 LEU
Chi-restraints excluded: chain D residue  217 ILE
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:    0.4980
   chunk 17 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.136735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.116476 restraints weight = 7446.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.99
r_work: 0.3552 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1704  Z= 0.128
  Angle     :  0.619   5.711   2346  Z= 0.299
  Chirality :  0.051   0.353    285
  Planarity :  0.004   0.032    300
  Dihedral  :  5.332  44.424    363
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.46 %
    Favored  : 72.07 %
  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:  0.01 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.37 (0.55), residues: 86
  loop : -0.22 (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   0.005   0.001   PHE D 138 
 TYR   0.010   0.001   TYR D 176 
 ARG   0.001   0.000   ARG D  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00400 (    7)
  link_NAG-ASN         : angle       2.10755 (   21)
  hydrogen bonds       : bond        0.03105 (   44)
  hydrogen bonds       : angle       5.37983 (   99)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.57824 (    2)
  covalent geometry    : bond        0.00304 ( 1696)
  covalent geometry    : angle       0.58902 ( 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
  70 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.243 
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: 0.8039 (mm-40) cc_final: 0.7559 (mm-40)
REVERT: D   62 LEU cc_start: 0.8863 (mt) cc_final: 0.8600 (mm)
REVERT: D   99 GLU cc_start: 0.7515 (mp0) cc_final: 0.7111 (mp0)
REVERT: D  132 GLU cc_start: 0.7913 (tt0) cc_final: 0.7686 (mt-10)
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 1.4912
  time to fit residues: 102.2465
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  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  200 LEU
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:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.135177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.114916 restraints weight = 7445.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.02
r_work: 0.3547 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1704  Z= 0.137
  Angle     :  0.620   5.965   2346  Z= 0.300
  Chirality :  0.051   0.344    285
  Planarity :  0.004   0.030    300
  Dihedral  :  5.334  44.337    363
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  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:  0.02 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.35 (0.56), residues: 85
  loop : -0.17 (0.63), residues: 113

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   0.005   0.001   PHE D 138 
 TYR   0.009   0.001   TYR D 176 
 ARG   0.001   0.000   ARG D 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00359 (    7)
  link_NAG-ASN         : angle       2.08917 (   21)
  hydrogen bonds       : bond        0.03113 (   44)
  hydrogen bonds       : angle       5.25087 (   99)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.63782 (    2)
  covalent geometry    : bond        0.00322 ( 1696)
  covalent geometry    : angle       0.59046 ( 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: 6
    poor density    : 65
  time to evaluate  : 0.240 
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: 0.8046 (mm-40) cc_final: 0.7547 (mm-40)
REVERT: D   62 LEU cc_start: 0.8870 (mt) cc_final: 0.8619 (mm)
REVERT: D   99 GLU cc_start: 0.7486 (mp0) cc_final: 0.7149 (mp0)
REVERT: D  200 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7725 (tm)
REVERT: D  216 GLU cc_start: 0.6779 (tt0) cc_final: 0.5977 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 69
  average time/residue: 1.3188
  time to fit residues: 93.2983
Evaluate side-chains
  70 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  200 LEU
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:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.7980
   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 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 = 0.136125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.115134 restraints weight = 7556.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 3.09
r_work: 0.3512 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1704  Z= 0.150
  Angle     :  0.627   5.914   2346  Z= 0.306
  Chirality :  0.051   0.347    285
  Planarity :  0.005   0.048    300
  Dihedral  :  5.491  44.638    363
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 26.82 %
    Favored  : 69.83 %
  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: -0.12 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.23 (0.55), residues: 85
  loop : -0.24 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 179 
 HIS   0.002   0.001   HIS D 139 
 PHE   0.005   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        0.00372 (    7)
  link_NAG-ASN         : angle       2.09073 (   21)
  hydrogen bonds       : bond        0.03119 (   44)
  hydrogen bonds       : angle       5.23699 (   99)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       1.32027 (    2)
  covalent geometry    : bond        0.00352 ( 1696)
  covalent geometry    : angle       0.59634 ( 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
  65 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.241 
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: 0.7528 (mm-40)
REVERT: D   62 LEU cc_start: 0.8897 (mt) cc_final: 0.8637 (mm)
REVERT: D   99 GLU cc_start: 0.7480 (mp0) cc_final: 0.7184 (mp0)
REVERT: D  216 GLU cc_start: 0.6877 (tt0) cc_final: 0.6051 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 62
  average time/residue: 1.5141
  time to fit residues: 96.0354
Evaluate side-chains
  64 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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
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:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0370
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.136013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.115411 restraints weight = 7395.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 3.06
r_work: 0.3509 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1704  Z= 0.143
  Angle     :  0.624   5.804   2346  Z= 0.306
  Chirality :  0.051   0.340    285
  Planarity :  0.005   0.048    300
  Dihedral  :  5.620  45.236    363
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 28.49 %
    Favored  : 68.72 %
  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 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.04 (0.55), residues: 87
  loop : -0.30 (0.64), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 179 
 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   0.002   0.000   ARG D 225 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00380 (    7)
  link_NAG-ASN         : angle       2.05113 (   21)
  hydrogen bonds       : bond        0.02986 (   44)
  hydrogen bonds       : angle       5.15935 (   99)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       1.24659 (    2)
  covalent geometry    : bond        0.00339 ( 1696)
  covalent geometry    : angle       0.59466 ( 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
  64 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.217 
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: 0.8047 (mm-40) cc_final: 0.7517 (mm-40)
REVERT: D   62 LEU cc_start: 0.8889 (mt) cc_final: 0.8647 (mm)
REVERT: D   99 GLU cc_start: 0.7466 (mp0) cc_final: 0.7195 (mp0)
REVERT: D  229 VAL cc_start: 0.8719 (t) cc_final: 0.8274 (m)
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 1.5549
  time to fit residues: 96.9419
Evaluate side-chains
  63 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   65 TYR
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:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.1980
   chunk 2 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D  61 GLN
** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.135439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.114415 restraints weight = 7340.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 3.04
r_work: 0.3485 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.4025

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= 0.128
  Angle     :  0.617   5.573   2346  Z= 0.305
  Chirality :  0.051   0.328    285
  Planarity :  0.005   0.046    300
  Dihedral  :  5.862  45.031    363
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 29.61 %
    Favored  : 67.60 %
  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:  0.10 (0.55), residues: 87
  loop : -0.26 (0.64), 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   0.004   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        0.00356 (    7)
  link_NAG-ASN         : angle       1.94018 (   21)
  hydrogen bonds       : bond        0.02849 (   44)
  hydrogen bonds       : angle       4.98192 (   99)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       1.01010 (    2)
  covalent geometry    : bond        0.00303 ( 1696)
  covalent geometry    : angle       0.59147 ( 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
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.239 
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: 0.8057 (mm-40) cc_final: 0.7503 (mm-40)
REVERT: D   62 LEU cc_start: 0.8883 (mt) cc_final: 0.8625 (mm)
REVERT: D   99 GLU cc_start: 0.7493 (mp0) cc_final: 0.7153 (mp0)
REVERT: D  229 VAL cc_start: 0.8695 (t) cc_final: 0.8241 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 65
  average time/residue: 1.4390
  time to fit residues: 95.7087
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   50 GLU
Chi-restraints excluded: chain D residue   65 TYR
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:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.134483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.114184 restraints weight = 7525.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 3.04
r_work: 0.3544 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.4258

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= 0.148
  Angle     :  0.640   5.615   2346  Z= 0.314
  Chirality :  0.051   0.318    285
  Planarity :  0.005   0.044    300
  Dihedral  :  6.245  49.932    363
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 31.28 %
    Favored  : 65.36 %
  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: -0.32 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.09 (0.55), residues: 87
  loop : -0.38 (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   0.003   0.001   PHE D 119 
 TYR   0.004   0.001   TYR D 213 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00356 (    7)
  link_NAG-ASN         : angle       1.99025 (   21)
  hydrogen bonds       : bond        0.03095 (   44)
  hydrogen bonds       : angle       5.06775 (   99)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       0.93231 (    2)
  covalent geometry    : bond        0.00353 ( 1696)
  covalent geometry    : angle       0.61458 ( 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: 6
    poor density    : 61
  time to evaluate  : 0.241 
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: 0.8034 (mm-40) cc_final: 0.7507 (mm-40)
REVERT: D   62 LEU cc_start: 0.8892 (mt) cc_final: 0.8646 (mm)
REVERT: D   99 GLU cc_start: 0.7477 (mp0) cc_final: 0.7146 (mp0)
REVERT: D  229 VAL cc_start: 0.8662 (t) cc_final: 0.8211 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 1.5588
  time to fit residues: 102.0272
Evaluate side-chains
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
D  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.136780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.116573 restraints weight = 7238.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.98
r_work: 0.3545 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.4329

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= 0.144
  Angle     :  0.647   5.536   2346  Z= 0.319
  Chirality :  0.051   0.324    285
  Planarity :  0.005   0.044    300
  Dihedral  :  6.731  59.974    363
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 30.17 %
    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: -0.44 (0.60), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.01 (0.55), residues: 87
  loop : -0.46 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 178 
 HIS   0.001   0.001   HIS D 139 
 PHE   0.003   0.001   PHE D  43 
 TYR   0.008   0.001   TYR D 176 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    7)
  link_NAG-ASN         : angle       2.01691 (   21)
  hydrogen bonds       : bond        0.03131 (   44)
  hydrogen bonds       : angle       5.08702 (   99)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       0.92069 (    2)
  covalent geometry    : bond        0.00344 ( 1696)
  covalent geometry    : angle       0.62117 ( 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
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.244 
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: 0.8188 (mm-40) cc_final: 0.7634 (mm-40)
REVERT: D   62 LEU cc_start: 0.8917 (mt) cc_final: 0.8682 (mm)
REVERT: D   99 GLU cc_start: 0.7668 (mp0) cc_final: 0.7321 (mp0)
REVERT: D  229 VAL cc_start: 0.8681 (t) cc_final: 0.8236 (m)
  outliers start: 6
  outliers final: 6
  residues processed: 65
  average time/residue: 1.5299
  time to fit residues: 101.6703
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  : 0.242 
-------------------------------------------------------------------------------
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  149 ILE
Chi-restraints excluded: chain D residue  152 ASN
Chi-restraints excluded: chain D residue  180 ILE
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:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
D  61 GLN
D 131 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.135340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.114872 restraints weight = 7330.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.00
r_work: 0.3546 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4442

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= 0.140
  Angle     :  0.653   5.533   2346  Z= 0.325
  Chirality :  0.050   0.295    285
  Planarity :  0.005   0.044    300
  Dihedral  :  6.382  53.011    363
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 29.61 %
    Favored  : 65.36 %
  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: -0.48 (0.60), residues: 198
  helix:  None (None), residues: 0
  sheet: -0.03 (0.54), residues: 89
  loop : -0.49 (0.63), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   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  82 
 ARG   0.002   0.000   ARG D 198 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00325 (    7)
  link_NAG-ASN         : angle       1.93689 (   21)
  hydrogen bonds       : bond        0.03126 (   44)
  hydrogen bonds       : angle       5.04186 (   99)
  SS BOND              : bond        0.00232 (    1)
  SS BOND              : angle       0.87724 (    2)
  covalent geometry    : bond        0.00332 ( 1696)
  covalent geometry    : angle       0.62906 ( 2323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3700.23 seconds
wall clock time: 64 minutes 13.85 seconds (3853.85 seconds total)