Starting phenix.real_space_refine
on Wed Sep 17 02:58:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xc5_38237/09_2025/8xc5_38237.cif"
  }
  resolution = 3.5
  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=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    1179      2.51       5
     N     320      2.21       5
     O     379      1.98       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: 1892
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 180
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 1, 'TRANS': 23}
    Chain: "B"
      Number of atoms: 1031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1031
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 625
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 5, 'TRANS': 73}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.55, per 1000 atoms: 0.29
  Number of scatterers: 1892
  At special positions: 0
  Unit cell: (50.4, 48.3, 94.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     379      8.00
     N     320      7.00
     C    1179      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 401 " - pdb=" SG  CYS B 461 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 422 " - pdb=" SG  CYS B 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 466 " - pdb=" SG  CYS B 473 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 229 " - pdb=" SG  CYS C 320 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 261 " - pdb=" SG  CYS C 284 " distance=2.07

  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 A 501 " - " ASN A 242 "
      " NAG B 601 " - " ASN B 362 "
      " NAG C 601 " - " ASN C 260 "
      " NAG C 602 " - " ASN C 291 "
  Time building additional restraints: 0.09
  Conformation dependent library (CDL) restraints added in 46.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  450

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 35.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 229
    Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 236
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 245
      removed outlier: 3.767A  pdb=" N   ASN C 315 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN C 319 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 245
      removed outlier: 3.767A  pdb=" N   ASN C 315 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN C 319 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.667A  pdb=" N   ALA B 356 " --> pdb=" O   GLY B 383 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY B 383 " --> pdb=" O   ALA B 356 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 445 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 227

    57 hydrogen bonds defined for protein.
    141 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: 0.14

  Time building geometry restraints manager: 0.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 628
        1.34 -     1.46: 387
        1.46 -     1.58: 888
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 1921
  Sorted by residual:
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.500 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" N   LEU A 241 "
       pdb=" CA  LEU A 241 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.24e-02 6.50e+03 5.45e+00
  bond pdb=" N   TYR C 322 "
       pdb=" CA  TYR C 322 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.51e-02 4.39e+03 5.35e+00
  bond pdb=" N   SER A 240 "
       pdb=" CA  SER A 240 "
    ideal  model  delta    sigma   weight residual
    1.457  1.479 -0.022 1.29e-02 6.01e+03 2.84e+00
  bond pdb=" N   PRO B 475 "
       pdb=" CA  PRO B 475 "
    ideal  model  delta    sigma   weight residual
    1.469  1.448  0.021 1.28e-02 6.10e+03 2.59e+00
  ... (remaining 1916 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 2440
        1.77 -     3.54: 134
        3.54 -     5.30: 21
        5.30 -     7.07: 4
        7.07 -     8.84: 3
  Bond angle restraints: 2602
  Sorted by residual:
  angle pdb=" C   ASN C 291 "
        pdb=" CA  ASN C 291 "
        pdb=" CB  ASN C 291 "
      ideal   model   delta    sigma   weight residual
     109.54  115.04   -5.50 1.84e+00 2.95e-01 8.95e+00
  angle pdb=" C1  NAG B 601 "
        pdb=" O5  NAG B 601 "
        pdb=" C5  NAG B 601 "
      ideal   model   delta    sigma   weight residual
     113.21  122.05   -8.84 3.00e+00 1.11e-01 8.68e+00
  angle pdb=" N   ASP C 228 "
        pdb=" CA  ASP C 228 "
        pdb=" C   ASP C 228 "
      ideal   model   delta    sigma   weight residual
     110.44  113.87   -3.43 1.20e+00 6.94e-01 8.19e+00
  angle pdb=" CA  ASP C 228 "
        pdb=" C   ASP C 228 "
        pdb=" O   ASP C 228 "
      ideal   model   delta    sigma   weight residual
     121.89  118.26    3.63 1.29e+00 6.01e-01 7.92e+00
  angle pdb=" C   PRO C 259 "
        pdb=" N   ASN C 260 "
        pdb=" CA  ASN C 260 "
      ideal   model   delta    sigma   weight residual
     122.15  117.42    4.73 1.74e+00 3.30e-01 7.39e+00
  ... (remaining 2597 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.42: 1082
       21.42 -    42.84: 129
       42.84 -    64.25: 17
       64.25 -    85.67: 3
       85.67 -   107.08: 4
  Dihedral angle restraints: 1235
    sinusoidal: 548
      harmonic: 687
  Sorted by residual:
  dihedral pdb=" CB  CYS B 422 "
           pdb=" SG  CYS B 422 "
           pdb=" SG  CYS B 477 "
           pdb=" CB  CYS B 477 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.80  -87.20     1      1.00e+01 1.00e-02 9.13e+01
  dihedral pdb=" CB  CYS B 466 "
           pdb=" SG  CYS B 466 "
           pdb=" SG  CYS B 473 "
           pdb=" CB  CYS B 473 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.59   74.59     1      1.00e+01 1.00e-02 7.05e+01
  dihedral pdb=" CA  CYS B 422 "
           pdb=" C   CYS B 422 "
           pdb=" N   SER B 423 "
           pdb=" CA  SER B 423 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.85   26.15     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 1232 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 283
       0.103 -    0.206: 25
       0.206 -    0.309: 2
       0.309 -    0.412: 0
       0.412 -    0.515: 1
  Chirality restraints: 311
  Sorted by residual:
  chirality pdb=" C1  NAG B 601 "
            pdb=" ND2 ASN B 362 "
            pdb=" C2  NAG B 601 "
            pdb=" O5  NAG B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.91    0.51 2.00e-01 2.50e+01 6.63e+00
  chirality pdb=" C1  NAG C 601 "
            pdb=" ND2 ASN C 260 "
            pdb=" C2  NAG C 601 "
            pdb=" O5  NAG C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.68    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C1  NAG C 602 "
            pdb=" ND2 ASN C 291 "
            pdb=" C2  NAG C 602 "
            pdb=" O5  NAG C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 308 not shown)

  Planarity restraints: 340
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 260 "   -0.057 2.00e-02 2.50e+03   5.93e-02 4.40e+01
        pdb=" CG  ASN C 260 "    0.019 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 260 "    0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 260 "    0.091 2.00e-02 2.50e+03
        pdb=" C1  NAG C 601 "   -0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 258 "   -0.048 5.00e-02 4.00e+02   7.25e-02 8.41e+00
        pdb=" N   PRO C 259 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO C 259 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 259 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 291 "   -0.023 2.00e-02 2.50e+03   2.21e-02 6.08e+00
        pdb=" CG  ASN C 291 "    0.010 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 291 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 291 "    0.033 2.00e-02 2.50e+03
        pdb=" C1  NAG C 602 "   -0.027 2.00e-02 2.50e+03
  ... (remaining 337 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 175
        2.74 -     3.28: 1869
        3.28 -     3.82: 2820
        3.82 -     4.36: 3254
        4.36 -     4.90: 5653
  Nonbonded interactions: 13771
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 359 "
            pdb=" O   ASN B 365 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" O   THR C 293 "
            pdb=" ND1 HIS C 294 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   GLU B 377 "
            pdb=" NE2 GLN B 446 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   THR C 300 "
            pdb=" OG1 THR C 300 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" NZ  LYS A 227 "
            pdb=" OE2 GLU B 462 "
     model   vdw
     2.296 3.120
  ... (remaining 13766 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 group one per residue
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:             1.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.770
  Find NCS groups from input model:        0.010
  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:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6355
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      :  0.008   0.168   1930  Z= 0.401
  Angle     :  1.407  32.602   2624  Z= 0.606
  Chirality :  0.065   0.515    311
  Planarity :  0.007   0.073    336
  Dihedral  : 17.640 107.083    770
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 31.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.35 %
    Favored  : 85.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 33.96 %
    Favored  : 66.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.61 (0.47), residues: 223
  helix:  None (None), residues: 0
  sheet: -2.19 (0.58), residues: 83
  loop : -3.85 (0.37), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 426 
 TYR   0.013   0.002   TYR B 402 
 PHE   0.014   0.002   PHE C 318 
 HIS   0.003   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 1921)
  covalent geometry    : angle       0.94208 ( 2602)
  SS BOND              : bond        0.01783 (    5)
  SS BOND              : angle       1.44949 (   10)
  hydrogen bonds       : bond        0.22545 (   44)
  hydrogen bonds       : angle      11.50349 (  141)
  link_NAG-ASN         : bond        0.12352 (    4)
  link_NAG-ASN         : angle      15.45712 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.041 
Fit side-chains
REVERT: B  447 MET cc_start: 0.8230 (tpp) cc_final: 0.7952 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0416
  time to fit residues: 2.7505
Evaluate side-chains
  49 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0570
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
B 453 HIS
B 470 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.186243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.163484 restraints weight = 2390.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.169255 restraints weight = 1374.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.173287 restraints weight = 896.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.176116 restraints weight = 629.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.178147 restraints weight = 463.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6512
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1930  Z= 0.184
  Angle     :  0.916  10.735   2624  Z= 0.444
  Chirality :  0.055   0.285    311
  Planarity :  0.006   0.062    336
  Dihedral  : 10.231  58.442    332
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.56 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 36.32 %
    Favored  : 57.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.21 (0.48), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.84 (0.57), residues: 82
  loop : -3.61 (0.39), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 399 
 TYR   0.013   0.002   TYR B 402 
 PHE   0.021   0.002   PHE C 318 
 HIS   0.005   0.001   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 1921)
  covalent geometry    : angle       0.89142 ( 2602)
  SS BOND              : bond        0.00530 (    5)
  SS BOND              : angle       1.61291 (   10)
  hydrogen bonds       : bond        0.05888 (   44)
  hydrogen bonds       : angle       7.81755 (  141)
  link_NAG-ASN         : bond        0.00350 (    4)
  link_NAG-ASN         : angle       2.96752 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: C  289 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6541 (tm-30)
  outliers start: 14
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0610
  time to fit residues: 4.6795
Evaluate side-chains
  57 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.181924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.157989 restraints weight = 2481.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.163703 restraints weight = 1440.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.167594 restraints weight = 954.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.170494 restraints weight = 691.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.172515 restraints weight = 519.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1930  Z= 0.174
  Angle     :  0.868   9.097   2624  Z= 0.416
  Chirality :  0.052   0.228    311
  Planarity :  0.005   0.050    336
  Dihedral  :  9.462  57.482    332
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers : 10.38 %
    Allowed  : 30.19 %
    Favored  : 59.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.99 (0.49), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.64 (0.58), residues: 82
  loop : -3.50 (0.41), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.014   0.002   TYR B 454 
 PHE   0.019   0.002   PHE C 318 
 HIS   0.004   0.001   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 1921)
  covalent geometry    : angle       0.84464 ( 2602)
  SS BOND              : bond        0.00499 (    5)
  SS BOND              : angle       1.03799 (   10)
  hydrogen bonds       : bond        0.05102 (   44)
  hydrogen bonds       : angle       7.02404 (  141)
  link_NAG-ASN         : bond        0.00527 (    4)
  link_NAG-ASN         : angle       3.03850 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
REVERT: B  388 GLN cc_start: 0.7984 (tp40) cc_final: 0.7709 (tt0)
REVERT: B  440 GLU cc_start: 0.6566 (tt0) cc_final: 0.6329 (tt0)
REVERT: C  289 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6697 (tm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0511
  time to fit residues: 4.0050
Evaluate side-chains
  60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  280 GLN
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  289 GLU
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0870
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.183005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.159740 restraints weight = 2324.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.165449 restraints weight = 1301.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.169511 restraints weight = 836.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.172341 restraints weight = 584.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.174411 restraints weight = 432.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   1930  Z= 0.157
  Angle     :  0.836   9.108   2624  Z= 0.409
  Chirality :  0.054   0.249    311
  Planarity :  0.004   0.046    336
  Dihedral  :  8.581  57.783    332
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.45 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  9.91 %
    Allowed  : 28.77 %
    Favored  : 61.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.91 (0.50), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.59 (0.59), residues: 82
  loop : -3.43 (0.41), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 399 
 TYR   0.014   0.001   TYR B 402 
 PHE   0.020   0.002   PHE C 307 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 1921)
  covalent geometry    : angle       0.81543 ( 2602)
  SS BOND              : bond        0.00395 (    5)
  SS BOND              : angle       0.88001 (   10)
  hydrogen bonds       : bond        0.04728 (   44)
  hydrogen bonds       : angle       6.48313 (  141)
  link_NAG-ASN         : bond        0.00395 (    4)
  link_NAG-ASN         : angle       2.84563 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 MET cc_start: 0.8135 (pmm) cc_final: 0.7584 (pmm)
REVERT: B  388 GLN cc_start: 0.8135 (tp40) cc_final: 0.7731 (tt0)
REVERT: B  425 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7544 (mp10)
REVERT: B  440 GLU cc_start: 0.6460 (tt0) cc_final: 0.6115 (tt0)
REVERT: C  258 ASP cc_start: 0.7017 (m-30) cc_final: 0.5952 (m-30)
  outliers start: 21
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0532
  time to fit residues: 4.1518
Evaluate side-chains
  60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  397 VAL
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  261 CYS
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 9 optimal weight:    0.2980
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0670
   chunk 11 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.181632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.159881 restraints weight = 2488.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.165467 restraints weight = 1447.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.169222 restraints weight = 950.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.171819 restraints weight = 672.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.173720 restraints weight = 501.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   1930  Z= 0.156
  Angle     :  0.830   9.089   2624  Z= 0.402
  Chirality :  0.052   0.247    311
  Planarity :  0.004   0.047    336
  Dihedral  :  8.468  57.576    332
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.45 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 29.72 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.82 (0.50), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.49 (0.58), residues: 82
  loop : -3.40 (0.41), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 442 
 TYR   0.012   0.001   TYR B 454 
 PHE   0.018   0.002   PHE C 307 
 HIS   0.002   0.001   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 1921)
  covalent geometry    : angle       0.80972 ( 2602)
  SS BOND              : bond        0.00397 (    5)
  SS BOND              : angle       0.78770 (   10)
  hydrogen bonds       : bond        0.04581 (   44)
  hydrogen bonds       : angle       6.21020 (  141)
  link_NAG-ASN         : bond        0.00350 (    4)
  link_NAG-ASN         : angle       2.80470 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  388 GLN cc_start: 0.8059 (tp40) cc_final: 0.7787 (tt0)
REVERT: B  425 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7575 (mp10)
REVERT: B  442 ARG cc_start: 0.7276 (ptp-170) cc_final: 0.6740 (mtt-85)
  outliers start: 15
  outliers final: 13
  residues processed: 62
  average time/residue: 0.0534
  time to fit residues: 3.9052
Evaluate side-chains
  60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  462 GLU
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  261 CYS
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.183854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.159797 restraints weight = 2433.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.165496 restraints weight = 1430.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.169419 restraints weight = 954.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.172251 restraints weight = 687.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.174349 restraints weight = 521.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   1930  Z= 0.160
  Angle     :  0.845   9.095   2624  Z= 0.412
  Chirality :  0.053   0.247    311
  Planarity :  0.004   0.045    336
  Dihedral  :  8.214  57.545    332
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.00 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  8.96 %
    Allowed  : 29.25 %
    Favored  : 61.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.82 (0.49), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.39 (0.57), residues: 82
  loop : -3.47 (0.41), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 426 
 TYR   0.013   0.001   TYR B 454 
 PHE   0.020   0.002   PHE C 318 
 HIS   0.002   0.001   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 1921)
  covalent geometry    : angle       0.82478 ( 2602)
  SS BOND              : bond        0.00386 (    5)
  SS BOND              : angle       0.70250 (   10)
  hydrogen bonds       : bond        0.04499 (   44)
  hydrogen bonds       : angle       6.23905 (  141)
  link_NAG-ASN         : bond        0.00214 (    4)
  link_NAG-ASN         : angle       2.84892 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 44
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: A  226 MET cc_start: 0.7901 (pmm) cc_final: 0.7527 (pmm)
REVERT: B  425 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7456 (tt0)
REVERT: B  442 ARG cc_start: 0.7201 (ptp-170) cc_final: 0.6728 (mtt-85)
REVERT: B  447 MET cc_start: 0.8312 (mmm) cc_final: 0.7771 (tmm)
REVERT: C  289 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6423 (tm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 58
  average time/residue: 0.0515
  time to fit residues: 3.5647
Evaluate side-chains
  56 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.179704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.157429 restraints weight = 2478.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.162580 restraints weight = 1509.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.166280 restraints weight = 1024.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.168908 restraints weight = 743.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.170707 restraints weight = 567.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   1930  Z= 0.191
  Angle     :  0.880   9.025   2624  Z= 0.430
  Chirality :  0.054   0.243    311
  Planarity :  0.005   0.048    336
  Dihedral  :  8.374  57.920    332
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  8.49 %
    Allowed  : 30.66 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.85 (0.48), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.44 (0.55), residues: 82
  loop : -3.47 (0.40), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 426 
 TYR   0.017   0.002   TYR B 454 
 PHE   0.025   0.003   PHE C 318 
 HIS   0.002   0.000   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 1921)
  covalent geometry    : angle       0.85952 ( 2602)
  SS BOND              : bond        0.00441 (    5)
  SS BOND              : angle       0.96773 (   10)
  hydrogen bonds       : bond        0.04536 (   44)
  hydrogen bonds       : angle       6.30427 (  141)
  link_NAG-ASN         : bond        0.00318 (    4)
  link_NAG-ASN         : angle       2.88827 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: B  425 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (mp10)
REVERT: B  442 ARG cc_start: 0.7127 (ptp-170) cc_final: 0.6792 (mtt-85)
REVERT: C  289 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6796 (tm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 58
  average time/residue: 0.0611
  time to fit residues: 4.0912
Evaluate side-chains
  59 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 43
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  370 ASP
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  221 HIS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4128 r_free = 0.4128 target = 0.180172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.159080 restraints weight = 2502.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.164137 restraints weight = 1526.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.167654 restraints weight = 1035.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.170149 restraints weight = 751.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.171883 restraints weight = 574.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   1930  Z= 0.173
  Angle     :  0.845   9.054   2624  Z= 0.414
  Chirality :  0.053   0.245    311
  Planarity :  0.005   0.048    336
  Dihedral  :  8.206  57.549    332
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.45 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  7.08 %
    Allowed  : 33.02 %
    Favored  : 59.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.74 (0.48), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.34 (0.56), residues: 82
  loop : -3.41 (0.41), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 426 
 TYR   0.013   0.002   TYR B 454 
 PHE   0.021   0.002   PHE C 318 
 HIS   0.002   0.001   HIS C 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 1921)
  covalent geometry    : angle       0.82513 ( 2602)
  SS BOND              : bond        0.00441 (    5)
  SS BOND              : angle       0.90732 (   10)
  hydrogen bonds       : bond        0.04449 (   44)
  hydrogen bonds       : angle       6.23502 (  141)
  link_NAG-ASN         : bond        0.00205 (    4)
  link_NAG-ASN         : angle       2.81801 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  388 GLN cc_start: 0.7998 (tp40) cc_final: 0.7778 (tt0)
REVERT: B  425 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7732 (mp10)
REVERT: C  289 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6852 (tm-30)
  outliers start: 15
  outliers final: 14
  residues processed: 56
  average time/residue: 0.0604
  time to fit residues: 3.9357
Evaluate side-chains
  56 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  370 ASP
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  294 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0370
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.4136 r_free = 0.4136 target = 0.180706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.159572 restraints weight = 2525.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.164624 restraints weight = 1540.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.168180 restraints weight = 1044.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.170544 restraints weight = 757.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.172450 restraints weight = 580.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.5110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   1930  Z= 0.170
  Angle     :  0.835   9.112   2624  Z= 0.409
  Chirality :  0.052   0.249    311
  Planarity :  0.005   0.049    336
  Dihedral  :  8.031  57.527    332
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 15.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  8.49 %
    Allowed  : 31.60 %
    Favored  : 59.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.51 (0.50), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.09 (0.58), residues: 81
  loop : -3.31 (0.42), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 426 
 TYR   0.014   0.001   TYR B 454 
 PHE   0.021   0.002   PHE C 318 
 HIS   0.002   0.001   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 1921)
  covalent geometry    : angle       0.81555 ( 2602)
  SS BOND              : bond        0.00387 (    5)
  SS BOND              : angle       0.77552 (   10)
  hydrogen bonds       : bond        0.04304 (   44)
  hydrogen bonds       : angle       6.12720 (  141)
  link_NAG-ASN         : bond        0.00242 (    4)
  link_NAG-ASN         : angle       2.78112 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  388 GLN cc_start: 0.7989 (tp40) cc_final: 0.7696 (tt0)
REVERT: B  442 ARG cc_start: 0.7014 (ptp-170) cc_final: 0.6764 (mtt-85)
  outliers start: 18
  outliers final: 17
  residues processed: 57
  average time/residue: 0.0517
  time to fit residues: 3.4963
Evaluate side-chains
  56 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  370 ASP
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  221 HIS
Chi-restraints excluded: chain C residue  223 LEU
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain C residue  312 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4139 r_free = 0.4139 target = 0.180915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.160244 restraints weight = 2527.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.165298 restraints weight = 1534.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.168808 restraints weight = 1036.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.171170 restraints weight = 748.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.173052 restraints weight = 569.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.4062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   1930  Z= 0.165
  Angle     :  0.837   9.124   2624  Z= 0.413
  Chirality :  0.053   0.249    311
  Planarity :  0.005   0.050    336
  Dihedral  :  7.896  57.326    332
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.90 %
    Favored  : 86.10 %
  Rotamer:
    Outliers :  8.49 %
    Allowed  : 32.08 %
    Favored  : 59.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.44 (0.50), residues: 223
  helix:  None (None), residues: 0
  sheet: -1.00 (0.58), residues: 81
  loop : -3.29 (0.42), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 290 
 TYR   0.012   0.002   TYR B 454 
 PHE   0.019   0.002   PHE C 318 
 HIS   0.002   0.000   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 1921)
  covalent geometry    : angle       0.81931 ( 2602)
  SS BOND              : bond        0.00360 (    5)
  SS BOND              : angle       0.74980 (   10)
  hydrogen bonds       : bond        0.04232 (   44)
  hydrogen bonds       : angle       5.97001 (  141)
  link_NAG-ASN         : bond        0.00184 (    4)
  link_NAG-ASN         : angle       2.70391 (   12)

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

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

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  446 Ramachandran restraints generated.
    223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 40
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  442 ARG cc_start: 0.7037 (ptp-170) cc_final: 0.6790 (mtt-85)
  outliers start: 18
  outliers final: 16
  residues processed: 57
  average time/residue: 0.0497
  time to fit residues: 3.3729
Evaluate side-chains
  55 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  248 ASN
Chi-restraints excluded: chain B residue  370 ASP
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  404 THR
Chi-restraints excluded: chain B residue  431 HIS
Chi-restraints excluded: chain B residue  454 TYR
Chi-restraints excluded: chain B residue  466 CYS
Chi-restraints excluded: chain C residue  221 HIS
Chi-restraints excluded: chain C residue  229 CYS
Chi-restraints excluded: chain C residue  236 VAL
Chi-restraints excluded: chain C residue  262 SER
Chi-restraints excluded: chain C residue  276 THR
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain C residue  312 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 21
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7240

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.179868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.159114 restraints weight = 2557.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.164171 restraints weight = 1548.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.167760 restraints weight = 1042.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.170098 restraints weight = 749.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.171918 restraints weight = 571.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
moved from start:          0.5410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   1930  Z= 0.179
  Angle     :  0.838   9.125   2624  Z= 0.415
  Chirality :  0.053   0.242    311
  Planarity :  0.005   0.051    336
  Dihedral  :  7.881  57.521    332
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.80 %
    Favored  : 85.20 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  : 31.60 %
    Favored  : 60.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.37 (0.50), residues: 223
  helix:  None (None), residues: 0
  sheet: -0.97 (0.59), residues: 81
  loop : -3.23 (0.42), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 426 
 TYR   0.015   0.001   TYR B 454 
 PHE   0.022   0.002   PHE C 318 
 HIS   0.002   0.000   HIS B 464 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 1921)
  covalent geometry    : angle       0.82049 ( 2602)
  SS BOND              : bond        0.00405 (    5)
  SS BOND              : angle       0.77941 (   10)
  hydrogen bonds       : bond        0.04341 (   44)
  hydrogen bonds       : angle       6.02850 (  141)
  link_NAG-ASN         : bond        0.00246 (    4)
  link_NAG-ASN         : angle       2.66661 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 668.91 seconds
wall clock time: 13 minutes 17.99 seconds (797.99 seconds total)