Starting phenix.real_space_refine
on Wed Sep 17 03:39:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gh6_51348/09_2025/9gh6_51348_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gh6_51348/09_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_51348/09_2025/9gh6_51348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gh6_51348/09_2025/9gh6_51348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gh6_51348/09_2025/9gh6_51348_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gh6_51348/09_2025/9gh6_51348_trim.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.73, per 1000 atoms: 0.23
  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: 0.27
  Conformation dependent library (CDL) restraints added in 72.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.10
  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: 0.65

  Time building geometry restraints manager: 0.39 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:             1.870
  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:             0.020
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.630
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.820
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (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
 ARG   0.004   0.001   ARG D  72 
 TYR   0.005   0.001   TYR D  82 
 PHE   0.002   0.000   PHE D  43 
 TRP   0.002   0.001   TRP D 178 
 HIS   0.000   0.000   HIS D  56 

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

*********************** 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  : 0.086 
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: 0.5749
  time to fit residues: 43.0076
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  : 0.099 
-------------------------------------------------------------------------------
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 12 optimal weight:    0.0470
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.135706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115003 restraints weight = 7691.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 3.18
r_work: 0.3466 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   1704  Z= 0.142
  Angle     :  0.645   5.614   2346  Z= 0.313
  Chirality :  0.050   0.325    285
  Planarity :  0.004   0.031    300
  Dihedral  :  6.144  48.377    365
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.79 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.78 (0.58), residues: 86
  loop : -0.20 (0.62), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 198 
 TYR   0.008   0.001   TYR D  82 
 PHE   0.007   0.001   PHE D 138 
 TRP   0.005   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 1696)
  covalent geometry    : angle       0.61423 ( 2323)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       0.54186 (    2)
  hydrogen bonds       : bond        0.03894 (   44)
  hydrogen bonds       : angle       6.04589 (   99)
  link_NAG-ASN         : bond        0.00546 (    7)
  link_NAG-ASN         : angle       2.16876 (   21)

*********************** 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: 5
    poor density    : 62
  time to evaluate  : 0.088 
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: 0.8114 (mm-40) cc_final: 0.7628 (mm-40)
REVERT: D   62 LEU cc_start: 0.8777 (mt) cc_final: 0.8504 (mm)
REVERT: D   99 GLU cc_start: 0.7616 (mp0) cc_final: 0.7056 (mp0)
REVERT: D  132 GLU cc_start: 0.7925 (tt0) cc_final: 0.7633 (mt-10)
REVERT: D  133 GLU cc_start: 0.7524 (mp0) cc_final: 0.7305 (mp0)
REVERT: D  178 TRP cc_start: 0.7149 (m100) cc_final: 0.6465 (m100)
REVERT: D  217 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7845 (pp)
REVERT: D  225 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7471 (mtt180)
  outliers start: 5
  outliers final: 2
  residues processed: 66
  average time/residue: 0.6782
  time to fit residues: 45.7767
Evaluate side-chains
  65 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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 13 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   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 = 0.3936 r_free = 0.3936 target = 0.138665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.118278 restraints weight = 7444.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.97
r_work: 0.3549 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2813

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= 0.148
  Angle     :  0.646   5.760   2346  Z= 0.309
  Chirality :  0.051   0.345    285
  Planarity :  0.004   0.031    300
  Dihedral  :  5.330  44.772    363
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.52 (0.56), residues: 86
  loop : -0.21 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  72 
 TYR   0.013   0.002   TYR D 176 
 PHE   0.008   0.001   PHE D 138 
 TRP   0.006   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 1696)
  covalent geometry    : angle       0.61482 ( 2323)
  SS BOND              : bond        0.00409 (    1)
  SS BOND              : angle       0.56352 (    2)
  hydrogen bonds       : bond        0.03612 (   44)
  hydrogen bonds       : angle       5.60201 (   99)
  link_NAG-ASN         : bond        0.00405 (    7)
  link_NAG-ASN         : angle       2.16868 (   21)

*********************** 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
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.090 
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: 0.8037 (mm-40) cc_final: 0.7529 (mm-40)
REVERT: D   62 LEU cc_start: 0.8808 (mt) cc_final: 0.8564 (mm)
REVERT: D   99 GLU cc_start: 0.7519 (mp0) cc_final: 0.7071 (mp0)
REVERT: D  132 GLU cc_start: 0.7876 (tt0) cc_final: 0.7606 (mt-10)
REVERT: D  225 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7486 (mtt180)
  outliers start: 5
  outliers final: 4
  residues processed: 67
  average time/residue: 0.7439
  time to fit residues: 50.8974
Evaluate side-chains
  66 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  217 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   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 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.135744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.115111 restraints weight = 7397.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 3.02
r_work: 0.3540 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3320

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= 0.161
  Angle     :  0.626   5.992   2346  Z= 0.304
  Chirality :  0.051   0.356    285
  Planarity :  0.004   0.032    300
  Dihedral  :  5.433  44.804    363
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 21.23 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.30 (0.55), residues: 86
  loop : -0.26 (0.63), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  72 
 TYR   0.011   0.002   TYR D 176 
 PHE   0.007   0.001   PHE D 138 
 TRP   0.005   0.001   TRP D 178 
 HIS   0.002   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 1696)
  covalent geometry    : angle       0.59295 ( 2323)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.55753 (    2)
  hydrogen bonds       : bond        0.03363 (   44)
  hydrogen bonds       : angle       5.47299 (   99)
  link_NAG-ASN         : bond        0.00411 (    7)
  link_NAG-ASN         : angle       2.19163 (   21)

*********************** 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  : 0.067 
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: 0.8042 (mm-40) cc_final: 0.7547 (mm-40)
REVERT: D   62 LEU cc_start: 0.8892 (mt) cc_final: 0.8630 (mm)
REVERT: D   99 GLU cc_start: 0.7494 (mp0) cc_final: 0.7149 (mp0)
REVERT: D  132 GLU cc_start: 0.7927 (tt0) cc_final: 0.7706 (mt-10)
  outliers start: 9
  outliers final: 8
  residues processed: 67
  average time/residue: 0.6694
  time to fit residues: 45.8640
Evaluate side-chains
  69 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
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
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 14 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0980
   chunk 11 optimal weight:    0.1980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.135558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.114968 restraints weight = 7441.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3656 rms_B_bonded: 3.05
r_work: 0.3553 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1704  Z= 0.116
  Angle     :  0.609   5.825   2346  Z= 0.296
  Chirality :  0.051   0.344    285
  Planarity :  0.004   0.030    300
  Dihedral  :  5.336  43.873    363
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.24 (0.56), residues: 80
  loop : -0.17 (0.61), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 225 
 TYR   0.009   0.001   TYR D 213 
 PHE   0.004   0.001   PHE D 138 
 TRP   0.005   0.001   TRP D 179 
 HIS   0.001   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 1696)
  covalent geometry    : angle       0.58022 ( 2323)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.68115 (    2)
  hydrogen bonds       : bond        0.02947 (   44)
  hydrogen bonds       : angle       5.08926 (   99)
  link_NAG-ASN         : bond        0.00378 (    7)
  link_NAG-ASN         : angle       2.02160 (   21)

*********************** 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: 7
    poor density    : 64
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7527 (mm-40)
REVERT: D   62 LEU cc_start: 0.8860 (mt) cc_final: 0.8605 (mm)
REVERT: D   99 GLU cc_start: 0.7463 (mp0) cc_final: 0.7126 (mp0)
REVERT: D  132 GLU cc_start: 0.7886 (tt0) cc_final: 0.7666 (mt-10)
REVERT: D  216 GLU cc_start: 0.6772 (tt0) cc_final: 0.5938 (tt0)
  outliers start: 7
  outliers final: 7
  residues processed: 67
  average time/residue: 0.6692
  time to fit residues: 45.8024
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  : 0.086 
-------------------------------------------------------------------------------
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   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  217 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3875 r_free = 0.3875 target = 0.134668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.113779 restraints weight = 7435.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.07
r_work: 0.3503 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   1704  Z= 0.164
  Angle     :  0.629   5.946   2346  Z= 0.309
  Chirality :  0.051   0.342    285
  Planarity :  0.005   0.046    300
  Dihedral  :  5.562  44.890    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 :  3.35 %
    Allowed  : 27.37 %
    Favored  : 69.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.62), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.47 (0.58), residues: 78
  loop : -0.39 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 225 
 TYR   0.005   0.001   TYR D 213 
 PHE   0.005   0.001   PHE D 138 
 TRP   0.007   0.001   TRP D 179 
 HIS   0.003   0.002   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 1696)
  covalent geometry    : angle       0.59858 ( 2323)
  SS BOND              : bond        0.00270 (    1)
  SS BOND              : angle       1.24027 (    2)
  hydrogen bonds       : bond        0.03223 (   44)
  hydrogen bonds       : angle       5.27302 (   99)
  link_NAG-ASN         : bond        0.00356 (    7)
  link_NAG-ASN         : angle       2.09280 (   21)

*********************** 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
  66 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.087 
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: 0.8071 (mm-40) cc_final: 0.7533 (mm-40)
REVERT: D   62 LEU cc_start: 0.8891 (mt) cc_final: 0.8630 (mm)
REVERT: D   99 GLU cc_start: 0.7471 (mp0) cc_final: 0.7186 (mp0)
REVERT: D  132 GLU cc_start: 0.7884 (tt0) cc_final: 0.7669 (mt-10)
REVERT: D  216 GLU cc_start: 0.6931 (tt0) cc_final: 0.6153 (tt0)
REVERT: D  229 VAL cc_start: 0.8744 (t) cc_final: 0.8299 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 63
  average time/residue: 0.7298
  time to fit residues: 46.9344
Evaluate side-chains
  65 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
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 18 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.136673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.116095 restraints weight = 7456.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 3.11
r_work: 0.3526 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3980

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= 0.144
  Angle     :  0.625   5.771   2346  Z= 0.306
  Chirality :  0.051   0.343    285
  Planarity :  0.005   0.041    300
  Dihedral  :  5.746  45.377    363
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 27.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.18 (0.55), residues: 85
  loop : -0.33 (0.63), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 225 
 TYR   0.010   0.001   TYR D 213 
 PHE   0.006   0.001   PHE D 165 
 TRP   0.008   0.001   TRP D 179 
 HIS   0.002   0.001   HIS D  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 1696)
  covalent geometry    : angle       0.59645 ( 2323)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       1.30275 (    2)
  hydrogen bonds       : bond        0.02998 (   44)
  hydrogen bonds       : angle       5.21355 (   99)
  link_NAG-ASN         : bond        0.00382 (    7)
  link_NAG-ASN         : angle       2.04744 (   21)

*********************** 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
  67 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.054 
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: 0.8051 (mm-40) cc_final: 0.7536 (mm-40)
REVERT: D   62 LEU cc_start: 0.8878 (mt) cc_final: 0.8658 (mm)
REVERT: D   99 GLU cc_start: 0.7468 (mp0) cc_final: 0.7234 (mp0)
REVERT: D  132 GLU cc_start: 0.7881 (tt0) cc_final: 0.7664 (mt-10)
REVERT: D  216 GLU cc_start: 0.6828 (tt0) cc_final: 0.6124 (tt0)
REVERT: D  229 VAL cc_start: 0.8735 (t) cc_final: 0.8298 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.6611
  time to fit residues: 43.8957
Evaluate side-chains
  65 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   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 = 0.3882 r_free = 0.3882 target = 0.135342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.114395 restraints weight = 7584.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 3.13
r_work: 0.3538 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4102

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= 0.152
  Angle     :  0.630   5.704   2346  Z= 0.310
  Chirality :  0.051   0.328    285
  Planarity :  0.005   0.039    300
  Dihedral  :  6.239  47.622    363
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.04 (0.56), residues: 87
  loop : -0.38 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 190 
 TYR   0.006   0.001   TYR D 213 
 PHE   0.005   0.001   PHE D 165 
 TRP   0.007   0.001   TRP D 179 
 HIS   0.002   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 1696)
  covalent geometry    : angle       0.60229 ( 2323)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       1.01772 (    2)
  hydrogen bonds       : bond        0.03050 (   44)
  hydrogen bonds       : angle       5.30215 (   99)
  link_NAG-ASN         : bond        0.00343 (    7)
  link_NAG-ASN         : angle       2.01800 (   21)

*********************** 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: 8
    poor density    : 60
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   60 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7512 (mm-40)
REVERT: D   62 LEU cc_start: 0.8902 (mt) cc_final: 0.8654 (mm)
REVERT: D   99 GLU cc_start: 0.7492 (mp0) cc_final: 0.7218 (mp0)
REVERT: D  216 GLU cc_start: 0.6910 (tt0) cc_final: 0.6135 (tt0)
REVERT: D  225 ARG cc_start: 0.7562 (mtt180) cc_final: 0.6606 (mtt180)
REVERT: D  229 VAL cc_start: 0.8717 (t) cc_final: 0.8268 (m)
  outliers start: 8
  outliers final: 8
  residues processed: 63
  average time/residue: 0.7604
  time to fit residues: 48.9005
Evaluate side-chains
  68 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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 1 optimal weight:    0.0870
   chunk 17 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0970
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.3884 r_free = 0.3884 target = 0.136717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115982 restraints weight = 7357.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.02
r_work: 0.3522 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1704  Z= 0.123
  Angle     :  0.630   5.494   2346  Z= 0.311
  Chirality :  0.050   0.314    285
  Planarity :  0.005   0.039    300
  Dihedral  :  6.704  59.661    363
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 27.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.61), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.06 (0.56), residues: 87
  loop : -0.45 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 207 
 TYR   0.005   0.001   TYR D 176 
 PHE   0.003   0.001   PHE D 165 
 TRP   0.005   0.001   TRP D 179 
 HIS   0.001   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 1696)
  covalent geometry    : angle       0.60505 ( 2323)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.91918 (    2)
  hydrogen bonds       : bond        0.02857 (   44)
  hydrogen bonds       : angle       5.03478 (   99)
  link_NAG-ASN         : bond        0.00343 (    7)
  link_NAG-ASN         : angle       1.92322 (   21)

*********************** 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
  73 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.065 
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: 0.8053 (mm-40) cc_final: 0.7512 (mm-40)
REVERT: D   62 LEU cc_start: 0.8868 (mt) cc_final: 0.8613 (mm)
REVERT: D   99 GLU cc_start: 0.7466 (mp0) cc_final: 0.7149 (mp0)
REVERT: D  216 GLU cc_start: 0.6788 (tt0) cc_final: 0.6080 (tt0)
REVERT: D  229 VAL cc_start: 0.8661 (t) cc_final: 0.8215 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 0.6896
  time to fit residues: 47.9360
Evaluate side-chains
  70 residues out of total 179 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
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  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 5 optimal weight:    0.0980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   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 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 = 0.135141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.114275 restraints weight = 7375.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 3.05
r_work: 0.3549 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4384

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= 0.135
  Angle     :  0.651   5.469   2346  Z= 0.323
  Chirality :  0.050   0.299    285
  Planarity :  0.005   0.037    300
  Dihedral  :  6.385  52.544    363
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 30.73 %
    Favored  : 65.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.60), residues: 198
  helix:  None (None), residues: 0
  sheet:  0.02 (0.55), residues: 87
  loop : -0.60 (0.61), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 198 
 TYR   0.005   0.001   TYR D 176 
 PHE   0.003   0.001   PHE D 119 
 TRP   0.005   0.001   TRP D 179 
 HIS   0.001   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 1696)
  covalent geometry    : angle       0.62618 ( 2323)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.94808 (    2)
  hydrogen bonds       : bond        0.03158 (   44)
  hydrogen bonds       : angle       5.00876 (   99)
  link_NAG-ASN         : bond        0.00332 (    7)
  link_NAG-ASN         : angle       1.95988 (   21)

********************** 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  : 0.085 
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: 0.8068 (mm-40) cc_final: 0.7522 (mm-40)
REVERT: D   62 LEU cc_start: 0.8877 (mt) cc_final: 0.8621 (mm)
REVERT: D   99 GLU cc_start: 0.7474 (mp0) cc_final: 0.7140 (mp0)
REVERT: D  108 LEU cc_start: 0.8184 (tt) cc_final: 0.7932 (tm)
REVERT: D  216 GLU cc_start: 0.6831 (tt0) cc_final: 0.6137 (tt0)
REVERT: D  229 VAL cc_start: 0.8651 (t) cc_final: 0.8192 (m)
  outliers start: 6
  outliers final: 7
  residues processed: 66
  average time/residue: 0.7211
  time to fit residues: 48.6026
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  : 0.073 
-------------------------------------------------------------------------------
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  180 ILE
Chi-restraints excluded: chain D residue  197 ASN
Chi-restraints excluded: chain D residue  209 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0370
   chunk 15 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.4458

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.135629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.114683 restraints weight = 7467.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 3.09
r_work: 0.3527 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4392

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= 0.127
  Angle     :  0.655   5.482   2346  Z= 0.324
  Chirality :  0.050   0.298    285
  Planarity :  0.005   0.037    300
  Dihedral  :  6.229  49.068    363
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.49 (0.60), residues: 198
  helix:  None (None), residues: 0
  sheet: -0.01 (0.54), residues: 89
  loop : -0.53 (0.62), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 198 
 TYR   0.005   0.001   TYR D 176 
 PHE   0.002   0.001   PHE D  43 
 TRP   0.005   0.001   TRP D 179 
 HIS   0.001   0.001   HIS D 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 1696)
  covalent geometry    : angle       0.62895 ( 2323)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       2.42256 (    2)
  hydrogen bonds       : bond        0.02937 (   44)
  hydrogen bonds       : angle       4.99505 (   99)
  link_NAG-ASN         : bond        0.00368 (    7)
  link_NAG-ASN         : angle       1.88777 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.01 seconds
wall clock time: 33 minutes 35.69 seconds (2015.69 seconds total)