Starting phenix.real_space_refine
on Fri May  9 23:34:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ikj_35514/05_2025/8ikj_35514.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ikj_35514/05_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_35514/05_2025/8ikj_35514.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ikj_35514/05_2025/8ikj_35514.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ikj_35514/05_2025/8ikj_35514.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ikj_35514/05_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-5687/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: 5.21, per 1000 atoms: 1.24
  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: 1.02
  Conformation dependent library (CDL) restraints added in 969.7 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: 0.48
  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: 1.21 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:             2.310
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     16.980
  Find NCS groups from input model:        0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.310
-------------------------------------------------------------------------------
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  : 0.486 
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: 0.3118
  time to fit residues: 29.8338
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  : 0.480 
-------------------------------------------------------------------------------
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:    0.4980
   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:    1.0784

-------------------------------------------------------------------------------
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 = 0.4382 r_free = 0.4382 target = 0.174905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.121903 restraints weight = 10495.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 3.56
r_work: 0.3344 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    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 = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   4302  Z= 0.259
  Angle     :  0.725  12.433   5852  Z= 0.358
  Chirality :  0.046   0.303    686
  Planarity :  0.005   0.060    724
  Dihedral  :  5.112  37.506    632
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  5.92 %
    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:  1.32 (0.36), residues: 529
  helix:  1.88 (0.30), residues: 269
  sheet:  0.35 (0.59), residues: 84
  loop : -0.37 (0.46), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 498 
 HIS   0.003   0.001   HIS R 539 
 PHE   0.017   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        0.00202 (    3)
  link_NAG-ASN         : angle       3.61010 (    9)
  hydrogen bonds       : bond        0.04224 (  259)
  hydrogen bonds       : angle       5.31726 (  749)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       2.87071 (    6)
  covalent geometry    : bond        0.00592 ( 4296)
  covalent geometry    : angle       0.70555 ( 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
  85 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8466 (mtm) cc_final: 0.8190 (mtm)
REVERT: R  338 MET cc_start: 0.8569 (mtm) cc_final: 0.8265 (mtm)
REVERT: R  407 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6982 (mmp)
REVERT: R  491 GLN cc_start: 0.7267 (tm-30) cc_final: 0.6883 (tm-30)
REVERT: R  537 MET cc_start: 0.6443 (tpt) cc_final: 0.5864 (tpt)
REVERT: R  540 TYR cc_start: 0.7683 (m-10) cc_final: 0.7354 (m-10)
REVERT: R  544 ASP cc_start: 0.6806 (p0) cc_final: 0.6555 (p0)
REVERT: R  576 GLN cc_start: 0.7358 (mm110) cc_final: 0.7039 (mm110)
REVERT: R  689 GLU cc_start: 0.6814 (tp30) cc_final: 0.6584 (tp30)
REVERT: R  792 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8330 (mtpp)
  outliers start: 6
  outliers final: 3
  residues processed: 83
  average time/residue: 0.2716
  time to fit residues: 26.2428
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  : 0.495 
-------------------------------------------------------------------------------
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    8.9990
   chunk 33 optimal weight:    0.5980
   chunk 24 optimal weight:    5.9990
   chunk 34 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 42 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0870
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4407 r_free = 0.4407 target = 0.176643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.123704 restraints weight = 15938.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 4.57
r_work: 0.3293 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4302  Z= 0.161
  Angle     :  0.642  10.836   5852  Z= 0.319
  Chirality :  0.042   0.223    686
  Planarity :  0.005   0.055    724
  Dihedral  :  5.060  44.975    632
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.02 %
    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 (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:  1.58 (0.37), residues: 529
  helix:  2.21 (0.31), residues: 262
  sheet:  0.47 (0.60), residues: 79
  loop : -0.35 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 498 
 HIS   0.003   0.000   HIS R 539 
 PHE   0.013   0.001   PHE R 627 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.002   0.000   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00252 (    3)
  link_NAG-ASN         : angle       2.41227 (    9)
  hydrogen bonds       : bond        0.03728 (  259)
  hydrogen bonds       : angle       5.06716 (  749)
  SS BOND              : bond        0.00253 (    3)
  SS BOND              : angle       1.81861 (    6)
  covalent geometry    : bond        0.00372 ( 4296)
  covalent geometry    : angle       0.63293 ( 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
  89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8511 (mtm) cc_final: 0.8222 (mtm)
REVERT: R  338 MET cc_start: 0.8659 (mtm) cc_final: 0.8332 (mtm)
REVERT: R  407 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7059 (mmp)
REVERT: R  423 GLN cc_start: 0.8736 (mt0) cc_final: 0.8474 (mt0)
REVERT: R  491 GLN cc_start: 0.7358 (tm-30) cc_final: 0.6995 (tm-30)
REVERT: R  537 MET cc_start: 0.6353 (tpt) cc_final: 0.5965 (tpt)
REVERT: R  540 TYR cc_start: 0.7763 (m-10) cc_final: 0.7423 (m-10)
REVERT: R  576 GLN cc_start: 0.7494 (mm110) cc_final: 0.7134 (mm110)
REVERT: R  792 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8426 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 86
  average time/residue: 0.2792
  time to fit residues: 27.7029
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  : 0.484 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 41 optimal weight:    0.2980
   chunk 23 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.177002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129334 restraints weight = 10021.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 3.24
r_work: 0.3393 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4302  Z= 0.190
  Angle     :  0.657  10.104   5852  Z= 0.330
  Chirality :  0.042   0.183    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.896  40.216    632
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.33 %
    Favored  : 90.35 %
  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:  1.46 (0.37), residues: 529
  helix:  2.09 (0.31), residues: 262
  sheet:  0.51 (0.61), residues: 79
  loop : -0.39 (0.46), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 498 
 HIS   0.002   0.001   HIS R 539 
 PHE   0.023   0.002   PHE R 623 
 TYR   0.009   0.001   TYR R 769 
 ARG   0.010   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00151 (    3)
  link_NAG-ASN         : angle       1.89050 (    9)
  hydrogen bonds       : bond        0.03693 (  259)
  hydrogen bonds       : angle       5.01947 (  749)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       2.57802 (    6)
  covalent geometry    : bond        0.00441 ( 4296)
  covalent geometry    : angle       0.64831 ( 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
  86 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8472 (mtm) cc_final: 0.8168 (mtm)
REVERT: R  338 MET cc_start: 0.8545 (mtm) cc_final: 0.8246 (mtm)
REVERT: R  407 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.7094 (mmp)
REVERT: R  491 GLN cc_start: 0.7229 (tm-30) cc_final: 0.6667 (tm-30)
REVERT: R  540 TYR cc_start: 0.7727 (m-10) cc_final: 0.7376 (m-10)
REVERT: R  544 ASP cc_start: 0.6651 (p0) cc_final: 0.6323 (p0)
REVERT: R  576 GLN cc_start: 0.7385 (mm110) cc_final: 0.7053 (mm110)
REVERT: R  630 MET cc_start: 0.7664 (tpt) cc_final: 0.7144 (tpt)
REVERT: R  792 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8389 (mtpp)
  outliers start: 6
  outliers final: 3
  residues processed: 83
  average time/residue: 0.2807
  time to fit residues: 26.8741
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  : 0.450 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 8 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 21 optimal weight:    8.9990
   chunk 51 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.5182

-------------------------------------------------------------------------------
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 = 0.4416 r_free = 0.4416 target = 0.176379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.124576 restraints weight = 10500.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 3.39
r_work: 0.3405 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3407
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2278

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= 0.156
  Angle     :  0.677  11.044   5852  Z= 0.335
  Chirality :  0.042   0.199    686
  Planarity :  0.004   0.054    724
  Dihedral  :  4.731  35.731    632
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  9.43 %
    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 (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:  1.46 (0.37), residues: 529
  helix:  2.15 (0.31), residues: 262
  sheet:  0.32 (0.60), residues: 80
  loop : -0.41 (0.46), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 498 
 HIS   0.003   0.000   HIS R 539 
 PHE   0.024   0.002   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.011   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    3)
  link_NAG-ASN         : angle       1.56925 (    9)
  hydrogen bonds       : bond        0.03562 (  259)
  hydrogen bonds       : angle       4.98449 (  749)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       1.97600 (    6)
  covalent geometry    : bond        0.00367 ( 4296)
  covalent geometry    : angle       0.67243 ( 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
  83 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8457 (mtm) cc_final: 0.8197 (mtm)
REVERT: R  338 MET cc_start: 0.8574 (mtm) cc_final: 0.8245 (mtm)
REVERT: R  407 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6780 (mmp)
REVERT: R  540 TYR cc_start: 0.7815 (m-10) cc_final: 0.7414 (m-10)
REVERT: R  544 ASP cc_start: 0.6621 (p0) cc_final: 0.6279 (p0)
REVERT: R  576 GLN cc_start: 0.7386 (mm110) cc_final: 0.7030 (mm110)
REVERT: R  792 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8372 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 81
  average time/residue: 0.2676
  time to fit residues: 25.1388
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  : 0.433 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 44 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.175614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.122721 restraints weight = 17165.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 4.87
r_work: 0.3313 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4302  Z= 0.183
  Angle     :  0.690  10.205   5852  Z= 0.343
  Chirality :  0.042   0.175    686
  Planarity :  0.004   0.053    724
  Dihedral  :  4.516  24.673    632
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.53 %
    Favored  : 88.16 %
  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:  1.35 (0.36), residues: 529
  helix:  2.06 (0.30), residues: 262
  sheet:  0.55 (0.62), residues: 74
  loop : -0.58 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 498 
 HIS   0.004   0.001   HIS R 539 
 PHE   0.022   0.002   PHE R 623 
 TYR   0.009   0.001   TYR R 769 
 ARG   0.003   0.000   ARG R 798 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    3)
  link_NAG-ASN         : angle       1.41444 (    9)
  hydrogen bonds       : bond        0.03624 (  259)
  hydrogen bonds       : angle       4.96638 (  749)
  SS BOND              : bond        0.00231 (    3)
  SS BOND              : angle       1.76537 (    6)
  covalent geometry    : bond        0.00430 ( 4296)
  covalent geometry    : angle       0.68591 ( 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: 6
    poor density    : 78
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8555 (mtm) cc_final: 0.8261 (mtm)
REVERT: R  338 MET cc_start: 0.8649 (mtm) cc_final: 0.8305 (mtm)
REVERT: R  407 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6800 (mmp)
REVERT: R  540 TYR cc_start: 0.7884 (m-10) cc_final: 0.7502 (m-10)
REVERT: R  544 ASP cc_start: 0.6782 (p0) cc_final: 0.6478 (p0)
REVERT: R  576 GLN cc_start: 0.7549 (mm110) cc_final: 0.7159 (mm110)
REVERT: R  792 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8410 (mtpp)
  outliers start: 6
  outliers final: 4
  residues processed: 82
  average time/residue: 0.2985
  time to fit residues: 28.1042
Evaluate side-chains
  80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0970
   chunk 20 optimal weight:    0.0470
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 = 0.4423 r_free = 0.4423 target = 0.177141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.127707 restraints weight = 11948.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 3.63
r_work: 0.3395 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4302  Z= 0.144
  Angle     :  0.697  10.808   5852  Z= 0.346
  Chirality :  0.041   0.168    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.444  23.120    632
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.18 %
    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:  1.55 (0.37), residues: 529
  helix:  2.27 (0.31), residues: 262
  sheet:  0.63 (0.62), residues: 74
  loop : -0.55 (0.45), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 498 
 HIS   0.003   0.000   HIS R 539 
 PHE   0.024   0.001   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.012   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    3)
  link_NAG-ASN         : angle       1.18963 (    9)
  hydrogen bonds       : bond        0.03358 (  259)
  hydrogen bonds       : angle       4.87772 (  749)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       2.43682 (    6)
  covalent geometry    : bond        0.00345 ( 4296)
  covalent geometry    : angle       0.69210 ( 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
  79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8422 (mtm) cc_final: 0.8148 (mtm)
REVERT: R  338 MET cc_start: 0.8557 (mtm) cc_final: 0.8225 (mtm)
REVERT: R  407 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6641 (mmp)
REVERT: R  540 TYR cc_start: 0.7812 (m-10) cc_final: 0.7540 (m-10)
REVERT: R  544 ASP cc_start: 0.6735 (p0) cc_final: 0.6404 (p0)
REVERT: R  576 GLN cc_start: 0.7447 (mm110) cc_final: 0.7053 (mm110)
REVERT: R  792 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8372 (mtpp)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 0.2687
  time to fit residues: 24.1428
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  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  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:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 47 optimal weight:    0.3980
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4414 r_free = 0.4414 target = 0.176329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.124646 restraints weight = 15618.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 4.74
r_work: 0.3290 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    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 = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2640

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= 0.220
  Angle     :  0.748  11.205   5852  Z= 0.374
  Chirality :  0.043   0.160    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.522  22.840    632
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.62 %
    Favored  : 87.06 %
  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:  1.33 (0.37), residues: 529
  helix:  2.02 (0.31), residues: 262
  sheet:  0.36 (0.60), residues: 83
  loop : -0.50 (0.47), residues: 184

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   0.022   0.002   PHE R 623 
 TYR   0.010   0.002   TYR R 683 
 ARG   0.010   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00087 (    3)
  link_NAG-ASN         : angle       1.15064 (    9)
  hydrogen bonds       : bond        0.03695 (  259)
  hydrogen bonds       : angle       4.97769 (  749)
  SS BOND              : bond        0.00280 (    3)
  SS BOND              : angle       2.56493 (    6)
  covalent geometry    : bond        0.00521 ( 4296)
  covalent geometry    : angle       0.74345 ( 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: 6
    poor density    : 75
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8553 (mtm) cc_final: 0.8255 (mtm)
REVERT: R  338 MET cc_start: 0.8672 (mtm) cc_final: 0.8338 (mtm)
REVERT: R  407 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6729 (mmp)
REVERT: R  537 MET cc_start: 0.6183 (tpt) cc_final: 0.5938 (tpt)
REVERT: R  544 ASP cc_start: 0.6886 (p0) cc_final: 0.6573 (p0)
REVERT: R  576 GLN cc_start: 0.7599 (mm110) cc_final: 0.7221 (mm110)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.2635
  time to fit residues: 23.9533
Evaluate side-chains
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 1 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0870
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 47 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   overall best weight:    0.3358

-------------------------------------------------------------------------------
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 = 0.4426 r_free = 0.4426 target = 0.177469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.126547 restraints weight = 9861.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 3.19
r_work: 0.3444 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3447
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3447 r_free = 0.3447    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3447
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4302  Z= 0.138
  Angle     :  0.704  11.496   5852  Z= 0.350
  Chirality :  0.041   0.156    686
  Planarity :  0.005   0.054    724
  Dihedral  :  4.398  23.348    632
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.50 %
    Favored  : 86.40 %
  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:  1.51 (0.37), residues: 529
  helix:  2.25 (0.31), residues: 262
  sheet:  0.17 (0.59), residues: 85
  loop : -0.40 (0.46), residues: 182

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   0.025   0.001   PHE R 623 
 TYR   0.012   0.001   TYR R 683 
 ARG   0.014   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    3)
  link_NAG-ASN         : angle       0.97494 (    9)
  hydrogen bonds       : bond        0.03383 (  259)
  hydrogen bonds       : angle       4.77878 (  749)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       2.04618 (    6)
  covalent geometry    : bond        0.00335 ( 4296)
  covalent geometry    : angle       0.70034 ( 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
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8344 (mtm) cc_final: 0.8100 (mtm)
REVERT: R  338 MET cc_start: 0.8492 (mtm) cc_final: 0.8177 (mtm)
REVERT: R  407 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6492 (mmp)
REVERT: R  537 MET cc_start: 0.6031 (tpt) cc_final: 0.5725 (tpt)
REVERT: R  544 ASP cc_start: 0.6619 (p0) cc_final: 0.6334 (p0)
REVERT: R  576 GLN cc_start: 0.7339 (mm110) cc_final: 0.6976 (mm110)
REVERT: R  680 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8247 (mtp85)
REVERT: R  791 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7808 (tmtt)
REVERT: R  792 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8366 (mtpp)
  outliers start: 5
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2720
  time to fit residues: 23.8120
Evaluate side-chains
  76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4413 r_free = 0.4413 target = 0.176466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.127285 restraints weight = 10324.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 3.33
r_work: 0.3382 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4302  Z= 0.211
  Angle     :  0.759  16.958   5852  Z= 0.371
  Chirality :  0.043   0.158    686
  Planarity :  0.005   0.052    724
  Dihedral  :  4.382  23.088    632
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 12.72 %
    Favored  : 86.18 %
  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 (0.37), residues: 529
  helix:  2.08 (0.31), residues: 261
  sheet:  0.09 (0.58), residues: 84
  loop : -0.45 (0.45), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 629 
 HIS   0.002   0.000   HIS R 539 
 PHE   0.026   0.002   PHE R 623 
 TYR   0.009   0.002   TYR R 769 
 ARG   0.009   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00083 (    3)
  link_NAG-ASN         : angle       1.04182 (    9)
  hydrogen bonds       : bond        0.03620 (  259)
  hydrogen bonds       : angle       4.93473 (  749)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       2.36795 (    6)
  covalent geometry    : bond        0.00503 ( 4296)
  covalent geometry    : angle       0.75476 ( 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
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  309 MET cc_start: 0.8454 (mtm) cc_final: 0.8172 (mtm)
REVERT: R  338 MET cc_start: 0.8595 (mtm) cc_final: 0.8270 (mtm)
REVERT: R  407 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6546 (mmp)
REVERT: R  537 MET cc_start: 0.6073 (tpt) cc_final: 0.5826 (tpt)
REVERT: R  544 ASP cc_start: 0.6719 (p0) cc_final: 0.6422 (p0)
REVERT: R  576 GLN cc_start: 0.7411 (mm110) cc_final: 0.7047 (mm110)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2723
  time to fit residues: 24.1128
Evaluate side-chains
  78 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   chunk 39 optimal weight:    0.2980
   chunk 13 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.3578

-------------------------------------------------------------------------------
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 = 0.4430 r_free = 0.4430 target = 0.177941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.127569 restraints weight = 7253.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.79
r_work: 0.3478 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3305 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4302  Z= 0.139
  Angle     :  0.721  16.582   5852  Z= 0.351
  Chirality :  0.041   0.149    686
  Planarity :  0.004   0.051    724
  Dihedral  :  4.256  23.027    632
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.50 %
    Favored  : 86.18 %
  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:  1.46 (0.37), residues: 529
  helix:  2.21 (0.31), residues: 262
  sheet: -0.01 (0.58), residues: 84
  loop : -0.34 (0.46), residues: 183

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   0.001   PHE R 623 
 TYR   0.007   0.001   TYR R 769 
 ARG   0.010   0.001   ARG R 277 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00265 (    3)
  link_NAG-ASN         : angle       0.91193 (    9)
  hydrogen bonds       : bond        0.03321 (  259)
  hydrogen bonds       : angle       4.79963 (  749)
  SS BOND              : bond        0.00250 (    3)
  SS BOND              : angle       1.99386 (    6)
  covalent geometry    : bond        0.00340 ( 4296)
  covalent geometry    : angle       0.71845 ( 5837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3314.08 seconds
wall clock time: 57 minutes 48.90 seconds (3468.90 seconds total)