Starting phenix.real_space_refine
on Sun Apr 27 02:43:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikj_35514/04_2025/8ikj_35514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikj_35514/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ikj_35514/04_2025/8ikj_35514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikj_35514/04_2025/8ikj_35514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikj_35514/04_2025/8ikj_35514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikj_35514/04_2025/8ikj_35514.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.00, per 1000 atoms: 1.19
  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: 0.96
  Conformation dependent library (CDL) restraints added in 920.6 milliseconds
  

  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: 0.37
  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: 1.17

  Time building geometry restraints manager: 1.16 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:                  0.010
  Normalize map: mean=0, sd=1:             0.690
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.890
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.830
-------------------------------------------------------------------------------
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 : 5.92
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.020   0.002   TRP R 498 
 HIS   0.002   0.000   HIS R 585 
 PHE   0.015   0.001   PHE R 627 
 TYR   0.009   0.001   TYR R 769 
 ARG   0.014   0.001   ARG R 277 

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

*********************** 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  : 0.640 
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: 0.2957
  time to fit residues: 28.4043
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  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:   40.0000
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0470
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9882

-------------------------------------------------------------------------------
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 = 0.4385 r_free = 0.4385 target = 0.175167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.124262 restraints weight = 10512.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 3.64
r_work: 0.3336 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3336
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3336 r_free = 0.3336    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1545

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= 0.240
  Angle     :  0.706  11.799   5852  Z= 0.349
  Chirality :  0.046   0.280    686
  Planarity :  0.005   0.060    724
  Dihedral  :  5.072  37.068    632
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.36 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.36), residues: 529
  helix:  1.93 (0.30), residues: 269
  sheet:  0.36 (0.59), residues: 84
  loop : -0.37 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 498 
 HIS   0.002   0.001   HIS R 539 
 PHE   0.016   0.002   PHE R 627 
 TYR   0.014   0.002   TYR R 660 
 ARG   0.007   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00175 (    3)
  link_NAG-ASN         : angle       3.63619 (    9)
  hydrogen bonds       : bond        0.04185 (  259)
  hydrogen bonds       : angle       5.29606 (  749)
  SS BOND              : bond        0.00458 (    3)
  SS BOND              : angle       2.82514 (    6)
  covalent geometry    : bond        0.00546 ( 4296)
  covalent geometry    : angle       0.68677 ( 5837)

*********************** 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
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8471 (mtm) cc_final: 0.8190 (mtm)
REVERT: R  338 MET cc_start: 0.8585 (mtm) cc_final: 0.8276 (mtm)
REVERT: R  407 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6993 (mmp)
REVERT: R  491 GLN cc_start: 0.7217 (tm-30) cc_final: 0.6865 (tm-30)
REVERT: R  537 MET cc_start: 0.6415 (tpt) cc_final: 0.5852 (tpt)
REVERT: R  540 TYR cc_start: 0.7657 (m-10) cc_final: 0.7310 (m-10)
REVERT: R  576 GLN cc_start: 0.7362 (mm110) cc_final: 0.7037 (mm110)
REVERT: R  689 GLU cc_start: 0.6823 (tp30) cc_final: 0.6603 (tp30)
REVERT: R  693 LEU cc_start: 0.8140 (tp) cc_final: 0.7932 (tp)
REVERT: R  792 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8292 (mtpp)
  outliers start: 4
  outliers final: 2
  residues processed: 82
  average time/residue: 0.2787
  time to fit residues: 26.4410
Evaluate side-chains
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.175840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.123061 restraints weight = 15966.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 4.79
r_work: 0.3279 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3278
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3278 r_free = 0.3278    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3278
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4302  Z= 0.199
  Angle     :  0.653  10.456   5852  Z= 0.327
  Chirality :  0.042   0.212    686
  Planarity :  0.005   0.056    724
  Dihedral  :  5.129  46.385    632
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  7.24 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.37), residues: 529
  helix:  1.98 (0.31), residues: 268
  sheet:  0.43 (0.60), residues: 79
  loop : -0.36 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R 498 
 HIS   0.004   0.001   HIS R 539 
 PHE   0.014   0.002   PHE R 627 
 TYR   0.010   0.002   TYR R 674 
 ARG   0.005   0.000   ARG R 579 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00112 (    3)
  link_NAG-ASN         : angle       2.29382 (    9)
  hydrogen bonds       : bond        0.03871 (  259)
  hydrogen bonds       : angle       5.15098 (  749)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       1.94270 (    6)
  covalent geometry    : bond        0.00459 ( 4296)
  covalent geometry    : angle       0.64415 ( 5837)

*********************** 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
  90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8534 (mtm) cc_final: 0.8227 (mtm)
REVERT: R  338 MET cc_start: 0.8664 (mtm) cc_final: 0.8335 (mtm)
REVERT: R  407 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7211 (mmp)
REVERT: R  423 GLN cc_start: 0.8769 (mt0) cc_final: 0.8546 (mt0)
REVERT: R  491 GLN cc_start: 0.7414 (tm-30) cc_final: 0.6876 (tm-30)
REVERT: R  537 MET cc_start: 0.6506 (tpt) cc_final: 0.6022 (tpt)
REVERT: R  540 TYR cc_start: 0.7827 (m-10) cc_final: 0.7498 (m-10)
REVERT: R  544 ASP cc_start: 0.6966 (p0) cc_final: 0.6294 (p0)
REVERT: R  546 LYS cc_start: 0.8567 (mttt) cc_final: 0.8279 (mtpp)
REVERT: R  576 GLN cc_start: 0.7498 (mm110) cc_final: 0.7133 (mm110)
REVERT: R  792 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8392 (mtpp)
  outliers start: 6
  outliers final: 3
  residues processed: 86
  average time/residue: 0.2896
  time to fit residues: 29.0124
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  : 0.434 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4389 r_free = 0.4389 target = 0.175402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123226 restraints weight = 10030.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 3.41
r_work: 0.3368 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4302  Z= 0.205
  Angle     :  0.668  10.397   5852  Z= 0.334
  Chirality :  0.042   0.188    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.878  39.905    632
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.77 %
    Favored  : 90.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.36), residues: 529
  helix:  2.08 (0.30), residues: 262
  sheet:  0.37 (0.60), residues: 80
  loop : -0.47 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 585 
 PHE   0.022   0.002   PHE R 623 
 TYR   0.009   0.001   TYR R 660 
 ARG   0.009   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00149 (    3)
  link_NAG-ASN         : angle       1.92427 (    9)
  hydrogen bonds       : bond        0.03766 (  259)
  hydrogen bonds       : angle       5.09663 (  749)
  SS BOND              : bond        0.00213 (    3)
  SS BOND              : angle       2.62555 (    6)
  covalent geometry    : bond        0.00475 ( 4296)
  covalent geometry    : angle       0.65928 ( 5837)

*********************** 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
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8337 (mtm) cc_final: 0.8073 (mtm)
REVERT: R  338 MET cc_start: 0.8438 (mtm) cc_final: 0.8122 (mtm)
REVERT: R  407 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6785 (mmp)
REVERT: R  423 GLN cc_start: 0.8666 (mt0) cc_final: 0.8425 (mt0)
REVERT: R  491 GLN cc_start: 0.7267 (tm-30) cc_final: 0.6626 (tm-30)
REVERT: R  537 MET cc_start: 0.6167 (tpt) cc_final: 0.5943 (tpt)
REVERT: R  540 TYR cc_start: 0.7744 (m-10) cc_final: 0.7393 (m-10)
REVERT: R  544 ASP cc_start: 0.6814 (p0) cc_final: 0.6161 (p0)
REVERT: R  546 LYS cc_start: 0.8570 (mttt) cc_final: 0.8272 (mtpp)
REVERT: R  576 GLN cc_start: 0.7340 (mm110) cc_final: 0.6964 (mm110)
REVERT: R  630 MET cc_start: 0.7544 (tpt) cc_final: 0.7021 (tpt)
REVERT: R  792 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8394 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 82
  average time/residue: 0.3572
  time to fit residues: 33.6361
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  : 1.146 
-------------------------------------------------------------------------------
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 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0870
   chunk 49 optimal weight:    0.7980
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    7.9990
   chunk 51 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4402 r_free = 0.4402 target = 0.176369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.123493 restraints weight = 10541.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 3.55
r_work: 0.3368 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.107         |
| 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) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4302  Z= 0.164
  Angle     :  0.654  10.886   5852  Z= 0.328
  Chirality :  0.041   0.168    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.800  38.137    632
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.99 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.37), residues: 529
  helix:  2.19 (0.31), residues: 262
  sheet:  0.17 (0.59), residues: 80
  loop : -0.45 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 674 
 ARG   0.011   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    3)
  link_NAG-ASN         : angle       1.54733 (    9)
  hydrogen bonds       : bond        0.03580 (  259)
  hydrogen bonds       : angle       5.05055 (  749)
  SS BOND              : bond        0.00207 (    3)
  SS BOND              : angle       1.99399 (    6)
  covalent geometry    : bond        0.00384 ( 4296)
  covalent geometry    : angle       0.64881 ( 5837)

*********************** 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
  88 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8406 (mtm) cc_final: 0.8131 (mtm)
REVERT: R  338 MET cc_start: 0.8551 (mtm) cc_final: 0.8216 (mtm)
REVERT: R  407 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6832 (mmp)
REVERT: R  491 GLN cc_start: 0.7223 (tm-30) cc_final: 0.6789 (tm-30)
REVERT: R  492 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: R  540 TYR cc_start: 0.7850 (m-10) cc_final: 0.7461 (m-10)
REVERT: R  544 ASP cc_start: 0.6765 (p0) cc_final: 0.6141 (p0)
REVERT: R  546 LYS cc_start: 0.8569 (mttt) cc_final: 0.8273 (mtpp)
REVERT: R  576 GLN cc_start: 0.7415 (mm110) cc_final: 0.7029 (mm110)
REVERT: R  792 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8391 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 86
  average time/residue: 0.2776
  time to fit residues: 27.6438
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  : 0.490 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.0070
   chunk 45 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0980
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
R 423 GLN
R 745 GLN
R 778 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.176035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.122233 restraints weight = 17303.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 5.01
r_work: 0.3268 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    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 = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4302  Z= 0.168
  Angle     :  0.670  10.518   5852  Z= 0.336
  Chirality :  0.041   0.179    686
  Planarity :  0.005   0.053    724
  Dihedral  :  4.638  32.256    632
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.65 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.37), residues: 529
  helix:  2.17 (0.31), residues: 262
  sheet:  0.45 (0.60), residues: 74
  loop : -0.57 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.006   0.001   TYR R 769 
 ARG   0.011   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00165 (    3)
  link_NAG-ASN         : angle       1.19504 (    9)
  hydrogen bonds       : bond        0.03529 (  259)
  hydrogen bonds       : angle       5.01145 (  749)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       1.71696 (    6)
  covalent geometry    : bond        0.00395 ( 4296)
  covalent geometry    : angle       0.66669 ( 5837)

*********************** 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
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8545 (mtm) cc_final: 0.8231 (mtm)
REVERT: R  338 MET cc_start: 0.8686 (mtm) cc_final: 0.8328 (mtm)
REVERT: R  407 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6899 (mmp)
REVERT: R  540 TYR cc_start: 0.7982 (m-10) cc_final: 0.7553 (m-10)
REVERT: R  544 ASP cc_start: 0.7024 (p0) cc_final: 0.6403 (p0)
REVERT: R  546 LYS cc_start: 0.8618 (mttt) cc_final: 0.8311 (mtpp)
REVERT: R  576 GLN cc_start: 0.7571 (mm110) cc_final: 0.7146 (mm110)
REVERT: R  792 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8394 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 82
  average time/residue: 0.2699
  time to fit residues: 25.7262
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  : 0.456 
-------------------------------------------------------------------------------
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 44 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.175741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.123765 restraints weight = 12048.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.88
r_work: 0.3338 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    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 = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4302  Z= 0.202
  Angle     :  0.701  10.788   5852  Z= 0.353
  Chirality :  0.042   0.153    686
  Planarity :  0.005   0.073    724
  Dihedral  :  4.485  23.345    632
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.18 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.36), residues: 529
  helix:  2.06 (0.31), residues: 262
  sheet:  0.46 (0.60), residues: 74
  loop : -0.60 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.009   0.001   TYR R 674 
 ARG   0.010   0.001   ARG R 435 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00088 (    3)
  link_NAG-ASN         : angle       1.12671 (    9)
  hydrogen bonds       : bond        0.03654 (  259)
  hydrogen bonds       : angle       5.06761 (  749)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       2.65567 (    6)
  covalent geometry    : bond        0.00477 ( 4296)
  covalent geometry    : angle       0.69561 ( 5837)

*********************** 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
  84 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8423 (mtm) cc_final: 0.8134 (mtm)
REVERT: R  338 MET cc_start: 0.8542 (mtm) cc_final: 0.8211 (mtm)
REVERT: R  407 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6735 (mmp)
REVERT: R  544 ASP cc_start: 0.6952 (p0) cc_final: 0.6225 (p0)
REVERT: R  546 LYS cc_start: 0.8616 (mttt) cc_final: 0.8317 (mtpp)
REVERT: R  576 GLN cc_start: 0.7456 (mm110) cc_final: 0.7066 (mm110)
REVERT: R  792 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8471 (mtpp)
  outliers start: 6
  outliers final: 5
  residues processed: 82
  average time/residue: 0.3154
  time to fit residues: 30.2649
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  646 GLN
Chi-restraints excluded: chain R residue  784 LEU
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 6 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 47 optimal weight:    0.3980
   chunk 19 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.175754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122051 restraints weight = 15840.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 4.79
r_work: 0.3270 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3270
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4302  Z= 0.192
  Angle     :  0.700  11.059   5852  Z= 0.351
  Chirality :  0.041   0.155    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.453  22.786    632
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.96 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 529
  helix:  2.10 (0.31), residues: 262
  sheet:  0.54 (0.61), residues: 73
  loop : -0.57 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.013   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    3)
  link_NAG-ASN         : angle       0.99753 (    9)
  hydrogen bonds       : bond        0.03648 (  259)
  hydrogen bonds       : angle       4.98256 (  749)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       2.49409 (    6)
  covalent geometry    : bond        0.00457 ( 4296)
  covalent geometry    : angle       0.69529 ( 5837)

*********************** 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: 7
    poor density    : 74
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8511 (mtm) cc_final: 0.8208 (mtm)
REVERT: R  338 MET cc_start: 0.8667 (mtm) cc_final: 0.8315 (mtm)
REVERT: R  407 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6728 (mmp)
REVERT: R  544 ASP cc_start: 0.7003 (p0) cc_final: 0.6396 (p0)
REVERT: R  546 LYS cc_start: 0.8623 (mttt) cc_final: 0.8326 (mtpp)
REVERT: R  576 GLN cc_start: 0.7554 (mm110) cc_final: 0.7151 (mm110)
REVERT: R  693 LEU cc_start: 0.7999 (tp) cc_final: 0.7793 (tp)
REVERT: R  792 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8472 (mtpp)
  outliers start: 7
  outliers final: 6
  residues processed: 78
  average time/residue: 0.2843
  time to fit residues: 25.7452
Evaluate side-chains
  81 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
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 10 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.175900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122461 restraints weight = 10021.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.55
r_work: 0.3368 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4302  Z= 0.190
  Angle     :  0.710  11.223   5852  Z= 0.356
  Chirality :  0.041   0.154    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.395  23.131    632
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.36), residues: 529
  helix:  2.08 (0.31), residues: 262
  sheet:  0.53 (0.61), residues: 73
  loop : -0.54 (0.44), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.026   0.002   PHE R 623 
 TYR   0.008   0.001   TYR R 674 
 ARG   0.009   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00126 (    3)
  link_NAG-ASN         : angle       0.98090 (    9)
  hydrogen bonds       : bond        0.03617 (  259)
  hydrogen bonds       : angle       4.97073 (  749)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       2.33733 (    6)
  covalent geometry    : bond        0.00454 ( 4296)
  covalent geometry    : angle       0.70588 ( 5837)

*********************** 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
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8374 (mtm) cc_final: 0.8083 (mtm)
REVERT: R  338 MET cc_start: 0.8564 (mtm) cc_final: 0.8224 (mtm)
REVERT: R  407 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6652 (mmp)
REVERT: R  435 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7068 (mtt90)
REVERT: R  543 GLU cc_start: 0.7275 (pm20) cc_final: 0.7074 (pm20)
REVERT: R  544 ASP cc_start: 0.6828 (p0) cc_final: 0.6160 (p0)
REVERT: R  546 LYS cc_start: 0.8576 (mttt) cc_final: 0.8298 (mtpp)
REVERT: R  576 GLN cc_start: 0.7413 (mm110) cc_final: 0.7027 (mm110)
REVERT: R  792 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8493 (mttm)
  outliers start: 7
  outliers final: 6
  residues processed: 77
  average time/residue: 0.2638
  time to fit residues: 23.6792
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
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 17 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0570
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 45 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.176248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.122664 restraints weight = 10483.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.55
r_work: 0.3367 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4302  Z= 0.172
  Angle     :  0.740  17.887   5852  Z= 0.362
  Chirality :  0.041   0.155    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.361  23.011    632
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.37), residues: 529
  helix:  2.12 (0.31), residues: 262
  sheet:  0.35 (0.59), residues: 79
  loop : -0.46 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.027   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.009   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00172 (    3)
  link_NAG-ASN         : angle       0.95081 (    9)
  hydrogen bonds       : bond        0.03566 (  259)
  hydrogen bonds       : angle       4.94657 (  749)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       2.23342 (    6)
  covalent geometry    : bond        0.00417 ( 4296)
  covalent geometry    : angle       0.73608 ( 5837)

********************** 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: 7
    poor density    : 73
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8362 (mtm) cc_final: 0.8084 (mtm)
REVERT: R  338 MET cc_start: 0.8536 (mtm) cc_final: 0.8201 (mtm)
REVERT: R  407 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6563 (mmp)
REVERT: R  435 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7105 (mtt90)
REVERT: R  544 ASP cc_start: 0.6833 (p0) cc_final: 0.6214 (p0)
REVERT: R  546 LYS cc_start: 0.8592 (mttt) cc_final: 0.8319 (mtpp)
REVERT: R  576 GLN cc_start: 0.7400 (mm110) cc_final: 0.7008 (mm110)
REVERT: R  792 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8437 (mttm)
  outliers start: 7
  outliers final: 6
  residues processed: 77
  average time/residue: 0.2831
  time to fit residues: 25.4043
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
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  646 GLN
Chi-restraints excluded: chain R residue  745 GLN
Chi-restraints excluded: chain R residue  784 LEU
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 37 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0870
   chunk 12 optimal weight:    6.9990
   chunk 26 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 39 optimal weight:    0.4980
   chunk 13 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
R 745 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.176792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.128827 restraints weight = 7383.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.75
r_work: 0.3410 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3409 r_free = 0.3409    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4302  Z= 0.158
  Angle     :  0.737  17.064   5852  Z= 0.366
  Chirality :  0.041   0.153    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.383  22.937    632
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.18 %
    Favored  : 87.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.37), residues: 529
  helix:  2.15 (0.31), residues: 262
  sheet:  0.16 (0.58), residues: 81
  loop : -0.37 (0.46), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 498 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.027   0.001   PHE R 623 
 TYR   0.006   0.001   TYR R 769 
 ARG   0.009   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00226 (    3)
  link_NAG-ASN         : angle       0.90877 (    9)
  hydrogen bonds       : bond        0.03493 (  259)
  hydrogen bonds       : angle       4.95737 (  749)
  SS BOND              : bond        0.00250 (    3)
  SS BOND              : angle       2.10851 (    6)
  covalent geometry    : bond        0.00386 ( 4296)
  covalent geometry    : angle       0.73440 ( 5837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3477.95 seconds
wall clock time: 60 minutes 48.00 seconds (3648.00 seconds total)