Starting phenix.real_space_refine
on Fri Aug 22 14:35:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikj_35514/08_2025/8ikj_35514.map"
  }
  resolution = 3.2
  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=   0.013
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      28      5.16       5
     C    2712      2.51       5
     N     702      2.21       5
     O     758      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4200
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "R"
      Number of atoms: 4158
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 532, 4147
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 20, 'TRANS': 511}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 532, 4147
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 20, 'TRANS': 511}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4226
    Chain: "R"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.06, per 1000 atoms: 0.49
  Number of scatterers: 4200
  At special positions: 0
  Unit cell: (79.98, 92.07, 119.97, 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      28     16.00
     O     758      8.00
     N     702      7.00
     C    2712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 495 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 513 " - pdb=" SG  CYS R 527 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 612 " - pdb=" SG  CYS R 684 " 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 R 901 " - " ASN R 413 "
      " NAG R 902 " - " ASN R 406 "
      " NAG R 903 " - " ASN R 520 "
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 306.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  988

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 3 sheets defined
      52.6% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'R' and resid 272 through 289
    Processing helix  chain 'R' and resid 293 through 311
    Processing helix  chain 'R' and resid 319 through 343
      removed outlier: 3.814A  pdb=" N   LYS R 343 " --> pdb=" O   ARG R 339 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 385 through 390
      removed outlier: 3.531A  pdb=" N   ALA R 389 " --> pdb=" O   TRP R 385 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLY R 390 " --> pdb=" O   ALA R 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 385 through 390'
    Processing helix  chain 'R' and resid 406 through 410
    Processing helix  chain 'R' and resid 419 through 431
    Processing helix  chain 'R' and resid 548 through 572
    Processing helix  chain 'R' and resid 577 through 601
    Processing helix  chain 'R' and resid 609 through 643
    Processing helix  chain 'R' and resid 651 through 674
      Proline residue:  R 663  - end of helix
    Processing helix  chain 'R' and resid 691 through 719
      removed outlier: 3.675A  pdb=" N   SER R 695 " --> pdb=" O   GLY R 691 " (cutoff:3.500A)
      Proline residue:  R 699  - end of helix
    Processing helix  chain 'R' and resid 735 through 756
    Processing helix  chain 'R' and resid 766 through 787
      removed outlier: 3.610A  pdb=" N   VAL R 770 " --> pdb=" O   VAL R 766 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 790 through 801
      removed outlier: 3.572A  pdb=" N   ARG R 794 " --> pdb=" O   ASN R 790 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 348 through 353
      removed outlier: 3.666A  pdb=" N   GLN R 365 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
      removed outlier: 6.078A  pdb=" N   VAL R 398 " --> pdb=" O   LEU R 450 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU R 450 " --> pdb=" O   VAL R 398 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   GLY R 400 " --> pdb=" O   ILE R 448 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE R 448 " --> pdb=" O   GLY R 400 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU R 402 " --> pdb=" O   ASN R 446 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 371 through 374
      removed outlier: 3.782A  pdb=" N   GLY R 517 " --> pdb=" O   THR R 524 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   GLN R 526 " --> pdb=" O   VAL R 515 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   VAL R 515 " --> pdb=" O   GLN R 526 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'R' and resid 436 through 438
      removed outlier: 4.520A  pdb=" N   SER R 532 " --> pdb=" O   TRP R 498 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA R 538 " --> pdb=" O   GLU R 492 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU R 492 " --> pdb=" O   ALA R 538 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    749 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: 0.61

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1088
        1.33 -     1.46: 869
        1.46 -     1.58: 2301
        1.58 -     1.70: 0
        1.70 -     1.82: 38
  Bond restraints: 4296
  Sorted by residual:
  bond pdb=" C   ALA R 412 "
       pdb=" N   ASN R 413 "
    ideal  model  delta    sigma   weight residual
    1.332  1.576 -0.244 1.40e-02 5.10e+03 3.03e+02
  bond pdb=" C   LYS R 519 "
       pdb=" N   ASN R 520 "
    ideal  model  delta    sigma   weight residual
    1.333  1.444 -0.111 1.39e-02 5.18e+03 6.42e+01
  bond pdb=" C   GLN R 405 "
       pdb=" N   ASN R 406 "
    ideal  model  delta    sigma   weight residual
    1.330  1.269  0.061 1.52e-02 4.33e+03 1.60e+01
  bond pdb=" C   ASN R 406 "
       pdb=" N   MET R 407 "
    ideal  model  delta    sigma   weight residual
    1.335  1.363 -0.029 1.33e-02 5.65e+03 4.74e+00
  bond pdb=" C   ASN R 520 "
       pdb=" N   GLY R 521 "
    ideal  model  delta    sigma   weight residual
    1.331  1.304  0.027 1.32e-02 5.74e+03 4.17e+00
  ... (remaining 4291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 5680
        1.88 -     3.76: 126
        3.76 -     5.63: 25
        5.63 -     7.51: 2
        7.51 -     9.39: 4
  Bond angle restraints: 5837
  Sorted by residual:
  angle pdb=" CA  GLN R 405 "
        pdb=" C   GLN R 405 "
        pdb=" N   ASN R 406 "
      ideal   model   delta    sigma   weight residual
     118.21  126.57   -8.36 1.36e+00 5.41e-01 3.78e+01
  angle pdb=" O   GLN R 405 "
        pdb=" C   GLN R 405 "
        pdb=" N   ASN R 406 "
      ideal   model   delta    sigma   weight residual
     122.46  114.48    7.98 1.37e+00 5.33e-01 3.40e+01
  angle pdb=" C   GLY R 647 "
        pdb=" N   GLN R 648 "
        pdb=" CA  GLN R 648 "
      ideal   model   delta    sigma   weight residual
     121.54  129.73   -8.19 1.91e+00 2.74e-01 1.84e+01
  angle pdb=" CA  LEU R 549 "
        pdb=" CB  LEU R 549 "
        pdb=" CG  LEU R 549 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  angle pdb=" CA  MET R 537 "
        pdb=" CB  MET R 537 "
        pdb=" CG  MET R 537 "
      ideal   model   delta    sigma   weight residual
     114.10  119.44   -5.34 2.00e+00 2.50e-01 7.13e+00
  ... (remaining 5832 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.04: 2306
       14.04 -    28.08: 193
       28.08 -    42.11: 61
       42.11 -    56.15: 14
       56.15 -    70.18: 6
  Dihedral angle restraints: 2580
    sinusoidal: 1048
      harmonic: 1532
  Sorted by residual:
  dihedral pdb=" CA  ASP R 761 "
           pdb=" C   ASP R 761 "
           pdb=" N   ASP R 762 "
           pdb=" CA  ASP R 762 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.47  -19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  MET R 537 "
           pdb=" C   MET R 537 "
           pdb=" N   ALA R 538 "
           pdb=" CA  ALA R 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.97  -19.03     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CB  CYS R 612 "
           pdb=" SG  CYS R 612 "
           pdb=" SG  CYS R 684 "
           pdb=" CB  CYS R 684 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -116.85   30.85     1      1.00e+01 1.00e-02 1.36e+01
  ... (remaining 2577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.302: 684
       0.302 -    0.603: 0
       0.603 -    0.905: 0
       0.905 -    1.206: 1
       1.206 -    1.508: 1
  Chirality restraints: 686
  Sorted by residual:
  chirality pdb=" C1  NAG R 902 "
            pdb=" ND2 ASN R 406 "
            pdb=" C2  NAG R 902 "
            pdb=" O5  NAG R 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.89   -1.51 2.00e-01 2.50e+01 5.68e+01
  chirality pdb=" C1  NAG R 903 "
            pdb=" ND2 ASN R 520 "
            pdb=" C2  NAG R 903 "
            pdb=" O5  NAG R 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.35   -1.05 2.00e-01 2.50e+01 2.73e+01
  chirality pdb=" CA  MET R 537 "
            pdb=" N   MET R 537 "
            pdb=" C   MET R 537 "
            pdb=" CB  MET R 537 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.48e-01
  ... (remaining 683 not shown)

  Planarity restraints: 727
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN R 413 "   -0.128 2.00e-02 2.50e+03   1.43e-01 2.55e+02
        pdb=" CG  ASN R 413 "    0.048 2.00e-02 2.50e+03
        pdb=" OD1 ASN R 413 "    0.028 2.00e-02 2.50e+03
        pdb=" ND2 ASN R 413 "    0.228 2.00e-02 2.50e+03
        pdb=" C1  NAG R 901 "   -0.175 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 348 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.12e+00
        pdb=" C   GLY R 348 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLY R 348 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO R 349 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA R 319 "   -0.047 5.00e-02 4.00e+02   7.11e-02 8.09e+00
        pdb=" N   PRO R 320 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO R 320 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO R 320 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 724 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 106
        2.71 -     3.26: 4103
        3.26 -     3.80: 6903
        3.80 -     4.35: 8293
        4.35 -     4.90: 14231
  Nonbonded interactions: 33636
  Sorted by model distance:
  nonbonded pdb=" O   ARG R 643 "
            pdb=" NE2 GLN R 646 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OG1 THR R 568 "
            pdb=" OH  TYR R 797 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" O   SER R 356 "
            pdb=" NE2 GLN R 405 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" NH1 ARG R 490 "
            pdb=" O   GLY R 605 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OE1 GLU R 295 "
            pdb=" NE2 GLN R 299 "
     model   vdw
     2.215 3.120
  ... (remaining 33631 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=0.50 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:             1.020
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     7.010
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7315
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      :  0.005   0.244   4302  Z= 0.337
  Angle     :  0.864  30.712   5852  Z= 0.406
  Chirality :  0.083   1.508    686
  Planarity :  0.006   0.071    724
  Dihedral  : 12.439  70.184   1583
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  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:  1.60 (0.36), residues: 529
  helix:  2.40 (0.31), residues: 266
  sheet:  0.66 (0.58), residues: 78
  loop : -0.79 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 277 
 TYR   0.009   0.001   TYR R 769 
 PHE   0.015   0.001   PHE R 627 
 TRP   0.020   0.002   TRP R 498 
 HIS   0.002   0.000   HIS R 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 ( 4296)
  covalent geometry    : angle       0.69715 ( 5837)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       1.53596 (    6)
  hydrogen bonds       : bond        0.09867 (  259)
  hydrogen bonds       : angle       5.75981 (  749)
  link_NAG-ASN         : bond        0.00740 (    3)
  link_NAG-ASN         : angle      12.97519 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.7964 (mtm) cc_final: 0.7721 (mtm)
REVERT: R  338 MET cc_start: 0.8201 (mtm) cc_final: 0.7958 (mtm)
REVERT: R  491 GLN cc_start: 0.6827 (tm-30) cc_final: 0.6241 (tm-30)
REVERT: R  537 MET cc_start: 0.5740 (tpt) cc_final: 0.5456 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1498
  time to fit residues: 14.3098
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0470
   chunk 50 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
R 271 HIS
R 299 GLN
R 646 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.177076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.126831 restraints weight = 7533.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.88
r_work: 0.3438 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4302  Z= 0.160
  Angle     :  0.670  12.401   5852  Z= 0.328
  Chirality :  0.044   0.313    686
  Planarity :  0.005   0.059    724
  Dihedral  :  4.933  36.666    632
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.36 %
    Favored  : 92.54 %
  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:  1.66 (0.37), residues: 529
  helix:  2.24 (0.31), residues: 268
  sheet:  0.66 (0.61), residues: 79
  loop : -0.42 (0.45), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R 277 
 TYR   0.009   0.001   TYR R 660 
 PHE   0.014   0.001   PHE R 627 
 TRP   0.017   0.001   TRP R 498 
 HIS   0.002   0.001   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4296)
  covalent geometry    : angle       0.64867 ( 5837)
  SS BOND              : bond        0.00451 (    3)
  SS BOND              : angle       2.66775 (    6)
  hydrogen bonds       : bond        0.03839 (  259)
  hydrogen bonds       : angle       5.13464 (  749)
  link_NAG-ASN         : bond        0.00332 (    3)
  link_NAG-ASN         : angle       3.80796 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8537 (mtm) cc_final: 0.8246 (mtm)
REVERT: R  338 MET cc_start: 0.8593 (mtm) cc_final: 0.8304 (mtm)
REVERT: R  407 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7000 (mmp)
REVERT: R  491 GLN cc_start: 0.7162 (tm-30) cc_final: 0.6843 (tm-30)
REVERT: R  537 MET cc_start: 0.6538 (tpt) cc_final: 0.5982 (tpt)
REVERT: R  540 TYR cc_start: 0.7675 (m-10) cc_final: 0.7299 (m-10)
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 0.1372
  time to fit residues: 13.0123
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 38 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 52 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.3168

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

Flipped N/Q/H residues before XYZ refinement:
R 271 HIS
R 778 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.177079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122320 restraints weight = 17510.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 4.69
r_work: 0.3324 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4302  Z= 0.124
  Angle     :  0.618  10.789   5852  Z= 0.307
  Chirality :  0.041   0.231    686
  Planarity :  0.005   0.055    724
  Dihedral  :  4.880  43.325    632
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  6.58 %
    Favored  : 91.89 %
  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:  1.82 (0.37), residues: 529
  helix:  2.53 (0.31), residues: 262
  sheet:  0.49 (0.60), residues: 79
  loop : -0.37 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 579 
 TYR   0.007   0.001   TYR R 683 
 PHE   0.012   0.001   PHE R 623 
 TRP   0.014   0.001   TRP R 498 
 HIS   0.003   0.000   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4296)
  covalent geometry    : angle       0.60905 ( 5837)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       1.61352 (    6)
  hydrogen bonds       : bond        0.03461 (  259)
  hydrogen bonds       : angle       4.91313 (  749)
  link_NAG-ASN         : bond        0.00400 (    3)
  link_NAG-ASN         : angle       2.51207 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8600 (mtm) cc_final: 0.8288 (mtm)
REVERT: R  407 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7037 (mmp)
REVERT: R  423 GLN cc_start: 0.8710 (mt0) cc_final: 0.8494 (mt0)
REVERT: R  491 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: R  537 MET cc_start: 0.6347 (tpt) cc_final: 0.5890 (tpt)
REVERT: R  540 TYR cc_start: 0.7819 (m-10) cc_final: 0.7479 (m-10)
REVERT: R  576 GLN cc_start: 0.7494 (mm110) cc_final: 0.7124 (mm110)
REVERT: R  680 ARG cc_start: 0.8635 (mtp85) cc_final: 0.8323 (mtp85)
REVERT: R  792 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8262 (mtpp)
  outliers start: 7
  outliers final: 5
  residues processed: 83
  average time/residue: 0.1448
  time to fit residues: 13.6901
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  440 ARG
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6384

-------------------------------------------------------------------------------
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 = 0.4434 r_free = 0.4434 target = 0.177722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.125809 restraints weight = 21169.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 5.62
r_work: 0.3297 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4302  Z= 0.169
  Angle     :  0.638  10.660   5852  Z= 0.318
  Chirality :  0.041   0.192    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.760  39.369    632
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.80 %
    Favored  : 92.11 %
  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:  1.70 (0.37), residues: 529
  helix:  2.35 (0.31), residues: 262
  sheet:  0.42 (0.62), residues: 79
  loop : -0.30 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG R 277 
 TYR   0.008   0.001   TYR R 660 
 PHE   0.015   0.001   PHE R 627 
 TRP   0.011   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4296)
  covalent geometry    : angle       0.63272 ( 5837)
  SS BOND              : bond        0.00200 (    3)
  SS BOND              : angle       1.52116 (    6)
  hydrogen bonds       : bond        0.03599 (  259)
  hydrogen bonds       : angle       4.92470 (  749)
  link_NAG-ASN         : bond        0.00159 (    3)
  link_NAG-ASN         : angle       1.83956 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8638 (mtm) cc_final: 0.8324 (mtm)
REVERT: R  407 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6998 (mmp)
REVERT: R  491 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7080 (tm-30)
REVERT: R  537 MET cc_start: 0.6333 (tpt) cc_final: 0.6078 (tpt)
REVERT: R  540 TYR cc_start: 0.7891 (m-10) cc_final: 0.7524 (m-10)
REVERT: R  544 ASP cc_start: 0.6921 (p0) cc_final: 0.6601 (p0)
REVERT: R  576 GLN cc_start: 0.7564 (mm110) cc_final: 0.7189 (mm110)
REVERT: R  792 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8338 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 83
  average time/residue: 0.1049
  time to fit residues: 10.0734
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.1980
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.4427 r_free = 0.4427 target = 0.177397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124361 restraints weight = 17165.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 4.92
r_work: 0.3334 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4302  Z= 0.148
  Angle     :  0.651  10.615   5852  Z= 0.324
  Chirality :  0.040   0.172    686
  Planarity :  0.004   0.053    724
  Dihedral  :  4.452  27.193    632
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.68 %
    Favored  : 91.23 %
  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:  1.68 (0.37), residues: 529
  helix:  2.40 (0.31), residues: 262
  sheet:  0.48 (0.62), residues: 74
  loop : -0.42 (0.46), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 277 
 TYR   0.005   0.001   TYR R 621 
 PHE   0.012   0.001   PHE R 627 
 TRP   0.010   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4296)
  covalent geometry    : angle       0.64493 ( 5837)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       2.34867 (    6)
  hydrogen bonds       : bond        0.03440 (  259)
  hydrogen bonds       : angle       4.91105 (  749)
  link_NAG-ASN         : bond        0.00254 (    3)
  link_NAG-ASN         : angle       1.46577 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8651 (mtm) cc_final: 0.8332 (mtm)
REVERT: R  407 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6849 (mmp)
REVERT: R  486 MET cc_start: 0.9067 (tmm) cc_final: 0.8360 (tmm)
REVERT: R  491 GLN cc_start: 0.7284 (tm-30) cc_final: 0.6748 (tm-30)
REVERT: R  537 MET cc_start: 0.6351 (tpt) cc_final: 0.5963 (tpt)
REVERT: R  540 TYR cc_start: 0.7893 (m-10) cc_final: 0.7577 (m-10)
REVERT: R  544 ASP cc_start: 0.6760 (p0) cc_final: 0.6434 (p0)
REVERT: R  792 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8379 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1247
  time to fit residues: 11.5828
Evaluate side-chains
  82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.177147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.124473 restraints weight = 15784.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 4.59
r_work: 0.3337 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3339
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3339 r_free = 0.3339    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3339
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4302  Z= 0.158
  Angle     :  0.661  11.540   5852  Z= 0.329
  Chirality :  0.040   0.157    686
  Planarity :  0.004   0.053    724
  Dihedral  :  4.390  24.040    632
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  7.89 %
    Favored  : 90.79 %
  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:  1.63 (0.37), residues: 529
  helix:  2.39 (0.31), residues: 262
  sheet:  0.34 (0.62), residues: 75
  loop : -0.44 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG R 277 
 TYR   0.008   0.001   TYR R 683 
 PHE   0.012   0.001   PHE R 627 
 TRP   0.009   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4296)
  covalent geometry    : angle       0.65689 ( 5837)
  SS BOND              : bond        0.00192 (    3)
  SS BOND              : angle       2.04055 (    6)
  hydrogen bonds       : bond        0.03462 (  259)
  hydrogen bonds       : angle       4.87893 (  749)
  link_NAG-ASN         : bond        0.00239 (    3)
  link_NAG-ASN         : angle       1.19778 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8600 (mtm) cc_final: 0.8292 (mtm)
REVERT: R  407 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6978 (mmp)
REVERT: R  491 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6718 (tm-30)
REVERT: R  537 MET cc_start: 0.6318 (tpt) cc_final: 0.6001 (tpt)
REVERT: R  540 TYR cc_start: 0.7838 (m-10) cc_final: 0.7561 (m-10)
REVERT: R  544 ASP cc_start: 0.6812 (p0) cc_final: 0.6464 (p0)
REVERT: R  576 GLN cc_start: 0.7535 (mm110) cc_final: 0.7156 (mm110)
REVERT: R  792 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8392 (mtpp)
  outliers start: 6
  outliers final: 4
  residues processed: 80
  average time/residue: 0.1176
  time to fit residues: 10.9001
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  784 LEU
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4418 r_free = 0.4418 target = 0.176499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.127376 restraints weight = 10451.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 3.48
r_work: 0.3353 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   4302  Z= 0.241
  Angle     :  0.708  10.962   5852  Z= 0.355
  Chirality :  0.042   0.145    686
  Planarity :  0.005   0.053    724
  Dihedral  :  4.479  22.815    632
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  8.99 %
    Favored  : 89.47 %
  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:  1.38 (0.37), residues: 529
  helix:  2.08 (0.31), residues: 262
  sheet:  0.46 (0.64), residues: 73
  loop : -0.51 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG R 277 
 TYR   0.009   0.002   TYR R 660 
 PHE   0.014   0.002   PHE R 645 
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 4296)
  covalent geometry    : angle       0.70412 ( 5837)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       2.15710 (    6)
  hydrogen bonds       : bond        0.03915 (  259)
  hydrogen bonds       : angle       5.01547 (  749)
  link_NAG-ASN         : bond        0.00062 (    3)
  link_NAG-ASN         : angle       1.14105 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8595 (mtm) cc_final: 0.8287 (mtm)
REVERT: R  407 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6723 (mmp)
REVERT: R  491 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6660 (tm-30)
REVERT: R  537 MET cc_start: 0.6316 (tpt) cc_final: 0.5973 (tpt)
REVERT: R  540 TYR cc_start: 0.7809 (m-10) cc_final: 0.7539 (m-10)
REVERT: R  544 ASP cc_start: 0.6723 (p0) cc_final: 0.6356 (p0)
REVERT: R  576 GLN cc_start: 0.7477 (mm110) cc_final: 0.7119 (mm110)
REVERT: R  687 ASP cc_start: 0.7769 (t70) cc_final: 0.7561 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 87
  average time/residue: 0.1191
  time to fit residues: 11.9783
Evaluate side-chains
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4422 r_free = 0.4422 target = 0.177149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.125798 restraints weight = 17020.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 4.90
r_work: 0.3286 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4302  Z= 0.169
  Angle     :  0.680  11.061   5852  Z= 0.341
  Chirality :  0.041   0.145    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.320  20.198    632
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.31 %
    Favored  : 88.82 %
  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:  1.51 (0.37), residues: 529
  helix:  2.25 (0.31), residues: 262
  sheet:  0.46 (0.62), residues: 73
  loop : -0.52 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG R 277 
 TYR   0.006   0.001   TYR R 769 
 PHE   0.011   0.001   PHE R 591 
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 4296)
  covalent geometry    : angle       0.67546 ( 5837)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       2.40203 (    6)
  hydrogen bonds       : bond        0.03458 (  259)
  hydrogen bonds       : angle       4.86566 (  749)
  link_NAG-ASN         : bond        0.00189 (    3)
  link_NAG-ASN         : angle       0.99988 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8667 (mtm) cc_final: 0.8359 (mtm)
REVERT: R  407 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6788 (mmp)
REVERT: R  491 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6638 (tm-30)
REVERT: R  537 MET cc_start: 0.6408 (tpt) cc_final: 0.5988 (tpt)
REVERT: R  540 TYR cc_start: 0.7930 (m-10) cc_final: 0.7692 (m-10)
REVERT: R  544 ASP cc_start: 0.6895 (p0) cc_final: 0.6530 (p0)
REVERT: R  576 GLN cc_start: 0.7597 (mm110) cc_final: 0.7198 (mm110)
REVERT: R  792 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8495 (mttm)
  outliers start: 4
  outliers final: 3
  residues processed: 79
  average time/residue: 0.1271
  time to fit residues: 11.6827
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0040
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.8796

-------------------------------------------------------------------------------
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 = 0.4410 r_free = 0.4410 target = 0.176110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.127157 restraints weight = 11874.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 3.50
r_work: 0.3362 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4302  Z= 0.222
  Angle     :  0.728  10.806   5852  Z= 0.367
  Chirality :  0.042   0.144    686
  Planarity :  0.005   0.058    724
  Dihedral  :  4.449  21.096    632
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.53 %
    Favored  : 88.60 %
  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:  1.37 (0.36), residues: 529
  helix:  2.08 (0.31), residues: 262
  sheet:  0.42 (0.62), residues: 75
  loop : -0.50 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 277 
 TYR   0.008   0.001   TYR R 769 
 PHE   0.012   0.002   PHE R 591 
 TRP   0.007   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 4296)
  covalent geometry    : angle       0.72266 ( 5837)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       2.67083 (    6)
  hydrogen bonds       : bond        0.03752 (  259)
  hydrogen bonds       : angle       4.96307 (  749)
  link_NAG-ASN         : bond        0.00082 (    3)
  link_NAG-ASN         : angle       1.07775 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8582 (mtm) cc_final: 0.8266 (mtm)
REVERT: R  407 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6742 (mmp)
REVERT: R  491 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6580 (tm-30)
REVERT: R  537 MET cc_start: 0.6276 (tpt) cc_final: 0.5882 (tpt)
REVERT: R  540 TYR cc_start: 0.7876 (m-10) cc_final: 0.7655 (m-10)
REVERT: R  544 ASP cc_start: 0.6696 (p0) cc_final: 0.6342 (p0)
REVERT: R  576 GLN cc_start: 0.7448 (mm110) cc_final: 0.7096 (mm110)
REVERT: R  630 MET cc_start: 0.7518 (tpt) cc_final: 0.7317 (mmm)
REVERT: R  792 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8508 (mttm)
  outliers start: 4
  outliers final: 3
  residues processed: 79
  average time/residue: 0.1083
  time to fit residues: 10.0233
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 43 optimal weight:    0.4980
   chunk 26 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4410 r_free = 0.4410 target = 0.176306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.125011 restraints weight = 12668.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 3.86
r_work: 0.3360 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3365
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3365 r_free = 0.3365    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3365
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4302  Z= 0.187
  Angle     :  0.714  11.530   5852  Z= 0.357
  Chirality :  0.041   0.146    686
  Planarity :  0.005   0.061    724
  Dihedral  :  4.420  21.705    632
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.18 %
    Favored  : 87.94 %
  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:  1.33 (0.37), residues: 529
  helix:  2.05 (0.31), residues: 262
  sheet:  0.27 (0.61), residues: 75
  loop : -0.48 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 277 
 TYR   0.007   0.001   TYR R 769 
 PHE   0.012   0.001   PHE R 627 
 TRP   0.010   0.001   TRP R 629 
 HIS   0.002   0.000   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 4296)
  covalent geometry    : angle       0.71023 ( 5837)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       2.34170 (    6)
  hydrogen bonds       : bond        0.03586 (  259)
  hydrogen bonds       : angle       4.89008 (  749)
  link_NAG-ASN         : bond        0.00102 (    3)
  link_NAG-ASN         : angle       0.98566 (    9)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  338 MET cc_start: 0.8609 (mtm) cc_final: 0.8291 (mtm)
REVERT: R  407 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6672 (mmp)
REVERT: R  491 GLN cc_start: 0.7237 (tm-30) cc_final: 0.6525 (tm-30)
REVERT: R  537 MET cc_start: 0.6215 (tpt) cc_final: 0.5899 (tpt)
REVERT: R  544 ASP cc_start: 0.6729 (p0) cc_final: 0.6358 (p0)
REVERT: R  576 GLN cc_start: 0.7459 (mm110) cc_final: 0.7074 (mm110)
REVERT: R  792 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8474 (mttm)
  outliers start: 4
  outliers final: 3
  residues processed: 78
  average time/residue: 0.1163
  time to fit residues: 10.5532
Evaluate side-chains
  82 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  407 MET
Chi-restraints excluded: chain R residue  548 THR
Chi-restraints excluded: chain R residue  551 THR
Chi-restraints excluded: chain R residue  791 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0470
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.1980
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.4418 r_free = 0.4418 target = 0.177048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.122752 restraints weight = 17006.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 4.55
r_work: 0.3339 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3336
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4302  Z= 0.159
  Angle     :  0.732  17.236   5852  Z= 0.359
  Chirality :  0.041   0.142    686
  Planarity :  0.005   0.061    724
  Dihedral  :  4.344  22.149    632
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.40 %
    Favored  : 87.72 %
  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:  1.41 (0.37), residues: 529
  helix:  2.15 (0.31), residues: 262
  sheet:  0.22 (0.60), residues: 75
  loop : -0.46 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG R 277 
 TYR   0.007   0.001   TYR R 769 
 PHE   0.012   0.001   PHE R 627 
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 4296)
  covalent geometry    : angle       0.72845 ( 5837)
  SS BOND              : bond        0.00225 (    3)
  SS BOND              : angle       2.12730 (    6)
  hydrogen bonds       : bond        0.03390 (  259)
  hydrogen bonds       : angle       4.89761 (  749)
  link_NAG-ASN         : bond        0.00168 (    3)
  link_NAG-ASN         : angle       0.93119 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1642.11 seconds
wall clock time: 28 minutes 41.66 seconds (1721.66 seconds total)