Starting phenix.real_space_refine
on Wed Jun  4 23:43:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hnc_34910/06_2025/8hnc_34910.cif"
  }
  resolution = 3.73
  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=   0.041
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      33      5.16       5
     C    2825      2.51       5
     N     678      2.21       5
     O     736      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4272
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4187
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 82}
          Link IDs: {'PTRANS': 21, 'TRANS': 548}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 249
          Unresolved non-hydrogen angles: 315
          Unresolved non-hydrogen dihedrals: 199
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 132
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'BLR': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.85, per 1000 atoms: 1.14
  Number of scatterers: 4272
  At special positions: 0
  Unit cell: (101.504, 59.904, 79.872, 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      33     16.00
     O     736      8.00
     N     678      7.00
     C    2825      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A 704 " - " ASN A 516 "
      " NAG B   1 " - " ASN A 503 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 551.8 milliseconds
  

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1036

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 1 sheets defined
      66.1% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 49
      removed outlier: 4.087A  pdb=" N   PHE A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 58
    Processing helix  chain 'A' and resid 62 through 79
      removed outlier: 4.505A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 3.946A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 91
      No H-bonds generated for 'chain 'A' and resid 89 through 91'
    Processing helix  chain 'A' and resid 92 through 113
    Processing helix  chain 'A' and resid 114 through 117
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 4.652A  pdb=" N   LYS A 125 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 165
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 4.085A  pdb=" N   VAL A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ARG A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 200
      removed outlier: 3.844A  pdb=" N   SER A 194 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   TYR A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 216
    Processing helix  chain 'A' and resid 217 through 231
    Processing helix  chain 'A' and resid 258 through 274
      removed outlier: 3.594A  pdb=" N   PHE A 262 " --> pdb=" O   TRP A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.815A  pdb=" N   LEU A 279 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 334
    Processing helix  chain 'A' and resid 335 through 366
      removed outlier: 5.253A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.425A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 400
      removed outlier: 3.757A  pdb=" N   GLY A 379 " --> pdb=" O   ASN A 375 " (cutoff:3.500A)
      Proline residue:  A 384  - end of helix
    Processing helix  chain 'A' and resid 403 through 426
      removed outlier: 3.767A  pdb=" N   PHE A 426 " --> pdb=" O   TYR A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 550
      removed outlier: 3.827A  pdb=" N   LYS A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A 535 " --> pdb=" O   THR A 531 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 563
      removed outlier: 3.537A  pdb=" N   VAL A 563 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 567 through 584
    Processing helix  chain 'A' and resid 586 through 597
    Processing helix  chain 'A' and resid 617 through 651
    Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481

    263 hydrogen bonds defined for protein.
    777 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: 1.13

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 664
        1.32 -     1.45: 1233
        1.45 -     1.57: 2432
        1.57 -     1.69: 0
        1.69 -     1.82: 49
  Bond restraints: 4378
  Sorted by residual:
  bond pdb=" CGD BLR A 701 "
       pdb=" O1D BLR A 701 "
    ideal  model  delta    sigma   weight residual
    1.231  1.308 -0.077 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" N   LEU A 545 "
       pdb=" CA  LEU A 545 "
    ideal  model  delta    sigma   weight residual
    1.459  1.505 -0.046 1.28e-02 6.10e+03 1.31e+01
  bond pdb=" C   TYR A 352 "
       pdb=" O   TYR A 352 "
    ideal  model  delta    sigma   weight residual
    1.236  1.198  0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" CA  LEU A 545 "
       pdb=" C   LEU A 545 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.35e-02 5.49e+03 9.96e+00
  bond pdb=" CA  TYR A 352 "
       pdb=" C   TYR A 352 "
    ideal  model  delta    sigma   weight residual
    1.524  1.483  0.041 1.32e-02 5.74e+03 9.53e+00
  ... (remaining 4373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 5701
        2.22 -     4.44: 206
        4.44 -     6.66: 32
        6.66 -     8.88: 9
        8.88 -    11.10: 3
  Bond angle restraints: 5951
  Sorted by residual:
  angle pdb=" N   VAL A 509 "
        pdb=" CA  VAL A 509 "
        pdb=" C   VAL A 509 "
      ideal   model   delta    sigma   weight residual
     110.62  118.68   -8.06 1.02e+00 9.61e-01 6.25e+01
  angle pdb=" N   ASN A 503 "
        pdb=" CA  ASN A 503 "
        pdb=" C   ASN A 503 "
      ideal   model   delta    sigma   weight residual
     111.56  122.66  -11.10 1.43e+00 4.89e-01 6.02e+01
  angle pdb=" C   THR A 186 "
        pdb=" N   PRO A 187 "
        pdb=" CA  PRO A 187 "
      ideal   model   delta    sigma   weight residual
     121.65  115.05    6.60 1.01e+00 9.80e-01 4.27e+01
  angle pdb=" C   TRP A 254 "
        pdb=" N   VAL A 255 "
        pdb=" CA  VAL A 255 "
      ideal   model   delta    sigma   weight residual
     122.99  114.19    8.80 1.39e+00 5.18e-01 4.01e+01
  angle pdb=" C   THR A 510 "
        pdb=" N   GLY A 511 "
        pdb=" CA  GLY A 511 "
      ideal   model   delta    sigma   weight residual
     121.58  116.85    4.73 8.60e-01 1.35e+00 3.02e+01
  ... (remaining 5946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.20: 2389
       21.20 -    42.40: 142
       42.40 -    63.60: 13
       63.60 -    84.79: 11
       84.79 -   105.99: 8
  Dihedral angle restraints: 2563
    sinusoidal: 936
      harmonic: 1627
  Sorted by residual:
  dihedral pdb=" CB  CYS A 459 "
           pdb=" SG  CYS A 459 "
           pdb=" SG  CYS A 506 "
           pdb=" CB  CYS A 506 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.59  -82.59     1      1.00e+01 1.00e-02 8.36e+01
  dihedral pdb=" CB  CYS A 142 "
           pdb=" SG  CYS A 142 "
           pdb=" SG  CYS A 463 "
           pdb=" CB  CYS A 463 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   14.62   78.38     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" C   LEU A 143 "
           pdb=" N   LEU A 143 "
           pdb=" CA  LEU A 143 "
           pdb=" CB  LEU A 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.31  -12.29     0      2.50e+00 1.60e-01 2.42e+01
  ... (remaining 2560 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.294: 691
       0.294 -    0.587: 3
       0.587 -    0.881: 0
       0.881 -    1.175: 0
       1.175 -    1.468: 1
  Chirality restraints: 695
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.93   -1.47 2.00e-02 2.50e+03 5.39e+03
  chirality pdb=" CA  ASN A 503 "
            pdb=" N   ASN A 503 "
            pdb=" C   ASN A 503 "
            pdb=" CB  ASN A 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.76e+00
  chirality pdb=" CA  ASN A 460 "
            pdb=" N   ASN A 460 "
            pdb=" C   ASN A 460 "
            pdb=" CB  ASN A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.24e+00
  ... (remaining 692 not shown)

  Planarity restraints: 728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "    0.313 2.00e-02 2.50e+03   2.66e-01 8.82e+02
        pdb=" C7  NAG B   2 "   -0.078 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "    0.181 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "   -0.463 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "    0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "    0.286 2.00e-02 2.50e+03   2.44e-01 7.46e+02
        pdb=" C7  NAG B   1 "   -0.063 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.018 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "   -0.412 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "    0.207 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 704 "   -0.159 2.00e-02 2.50e+03   1.31e-01 2.14e+02
        pdb=" C7  NAG A 704 "    0.045 2.00e-02 2.50e+03
        pdb=" C8  NAG A 704 "   -0.118 2.00e-02 2.50e+03
        pdb=" N2  NAG A 704 "    0.210 2.00e-02 2.50e+03
        pdb=" O7  NAG A 704 "    0.022 2.00e-02 2.50e+03
  ... (remaining 725 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 53
        2.64 -     3.21: 4287
        3.21 -     3.77: 6608
        3.77 -     4.34: 8538
        4.34 -     4.90: 13867
  Nonbonded interactions: 33353
  Sorted by model distance:
  nonbonded pdb=" ND  BLR A 701 "
            pdb=" O2A BLR A 701 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" O   MET A 233 "
            pdb=" N   ALA A 257 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ASN A 460 "
            pdb=" N   CYS A 463 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG  SER A 418 "
            pdb=" ND2 ASN A 544 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" ND1 HIS A 115 "
            pdb=" CD1 TRP A 259 "
     model   vdw
     2.364 3.340
  ... (remaining 33348 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.720
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.382   4388  Z= 0.463
  Angle     :  1.277  52.004   5974  Z= 0.691
  Chirality :  0.081   1.468    695
  Planarity :  0.015   0.266    726
  Dihedral  : 15.074 105.991   1506
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.11 %
    Favored  : 94.40 %
  Cbeta Deviations :  0.39 %
  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: -2.79 (0.31), residues: 562
  helix: -1.27 (0.24), residues: 343
  sheet:  None (None), residues: 0
  loop : -2.72 (0.37), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 258 
 HIS   0.002   0.001   HIS A  92 
 PHE   0.029   0.001   PHE A 591 
 TYR   0.025   0.002   TYR A 352 
 ARG   0.001   0.000   ARG A  57 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00145 (    2)
  link_NAG-ASN         : angle      10.72764 (    6)
  link_BETA1-4         : bond        0.38155 (    1)
  link_BETA1-4         : angle      31.45835 (    3)
  hydrogen bonds       : bond        0.15315 (  263)
  hydrogen bonds       : angle       7.41183 (  777)
  SS BOND              : bond        0.00877 (    7)
  SS BOND              : angle       1.36399 (   14)
  covalent geometry    : bond        0.00616 ( 4378)
  covalent geometry    : angle       1.00940 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8898 (tpt) cc_final: 0.8483 (tpp)
REVERT: A  185 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: A  381 ILE cc_start: 0.8682 (tp) cc_final: 0.8426 (tp)
REVERT: A  617 ASN cc_start: 0.7996 (t0) cc_final: 0.7607 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2441
  time to fit residues: 31.8297
Evaluate side-chains
  75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 544 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.168229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.117889 restraints weight = 4804.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.119861 restraints weight = 3777.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.120555 restraints weight = 3233.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4388  Z= 0.154
  Angle     :  0.692  14.006   5974  Z= 0.325
  Chirality :  0.043   0.265    695
  Planarity :  0.004   0.039    726
  Dihedral  :  8.761  85.736    680
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 14.11 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.48 (0.34), residues: 562
  helix:  0.59 (0.28), residues: 346
  sheet:  None (None), residues: 0
  loop : -1.81 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A  92 
 PHE   0.013   0.001   PHE A 591 
 TYR   0.029   0.002   TYR A 590 
 ARG   0.005   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00651 (    2)
  link_NAG-ASN         : angle       3.53071 (    6)
  link_BETA1-4         : bond        0.01022 (    1)
  link_BETA1-4         : angle       8.88723 (    3)
  hydrogen bonds       : bond        0.04671 (  263)
  hydrogen bonds       : angle       4.79194 (  777)
  SS BOND              : bond        0.00163 (    7)
  SS BOND              : angle       1.04141 (   14)
  covalent geometry    : bond        0.00349 ( 4378)
  covalent geometry    : angle       0.65247 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8982 (tpt) cc_final: 0.8542 (tpp)
REVERT: A  254 TRP cc_start: 0.7933 (t-100) cc_final: 0.7671 (t-100)
REVERT: A  381 ILE cc_start: 0.8707 (tp) cc_final: 0.8412 (tp)
REVERT: A  390 MET cc_start: 0.8380 (mmt) cc_final: 0.7798 (mmt)
  outliers start: 6
  outliers final: 3
  residues processed: 85
  average time/residue: 0.1713
  time to fit residues: 19.2788
Evaluate side-chains
  80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 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 = 0.3968 r_free = 0.3968 target = 0.184204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.127149 restraints weight = 4934.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.130768 restraints weight = 3275.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.132835 restraints weight = 2555.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4388  Z= 0.153
  Angle     :  0.627  10.401   5974  Z= 0.297
  Chirality :  0.042   0.270    695
  Planarity :  0.004   0.041    726
  Dihedral  :  7.432  83.083    680
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.03 %
    Favored  : 80.05 %
  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:  0.36 (0.36), residues: 562
  helix:  1.28 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.44 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A  54 
 PHE   0.013   0.001   PHE A 591 
 TYR   0.023   0.002   TYR A 590 
 ARG   0.006   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00188 (    2)
  link_NAG-ASN         : angle       3.81114 (    6)
  link_BETA1-4         : bond        0.00847 (    1)
  link_BETA1-4         : angle       6.60911 (    3)
  hydrogen bonds       : bond        0.04380 (  263)
  hydrogen bonds       : angle       4.43430 (  777)
  SS BOND              : bond        0.00127 (    7)
  SS BOND              : angle       0.65266 (   14)
  covalent geometry    : bond        0.00363 ( 4378)
  covalent geometry    : angle       0.59755 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8874 (tpt) cc_final: 0.8448 (tpp)
REVERT: A  170 MET cc_start: 0.7949 (mmm) cc_final: 0.7649 (mmm)
REVERT: A  176 MET cc_start: 0.8245 (tpp) cc_final: 0.7942 (mmt)
REVERT: A  254 TRP cc_start: 0.8105 (t-100) cc_final: 0.7809 (t-100)
REVERT: A  356 PHE cc_start: 0.7230 (m-80) cc_final: 0.6768 (t80)
REVERT: A  381 ILE cc_start: 0.8599 (tp) cc_final: 0.8304 (tp)
REVERT: A  390 MET cc_start: 0.8226 (mmt) cc_final: 0.7593 (mmt)
REVERT: A  504 CYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7513 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1381
  time to fit residues: 15.9734
Evaluate side-chains
  85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  422 TYR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.1980
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.187454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.130422 restraints weight = 5011.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.134006 restraints weight = 3263.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.136501 restraints weight = 2523.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4388  Z= 0.130
  Angle     :  0.594   9.515   5974  Z= 0.285
  Chirality :  0.041   0.219    695
  Planarity :  0.004   0.042    726
  Dihedral  :  7.084  79.445    680
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.00 %
    Favored  : 78.10 %
  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:  0.75 (0.36), residues: 562
  helix:  1.67 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -1.39 (0.40), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A  92 
 PHE   0.012   0.001   PHE A 591 
 TYR   0.024   0.002   TYR A 590 
 ARG   0.007   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    2)
  link_NAG-ASN         : angle       3.23535 (    6)
  link_BETA1-4         : bond        0.00285 (    1)
  link_BETA1-4         : angle       6.02706 (    3)
  hydrogen bonds       : bond        0.04077 (  263)
  hydrogen bonds       : angle       4.20292 (  777)
  SS BOND              : bond        0.00105 (    7)
  SS BOND              : angle       0.57946 (   14)
  covalent geometry    : bond        0.00297 ( 4378)
  covalent geometry    : angle       0.56935 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8782 (tpt) cc_final: 0.8406 (tpp)
REVERT: A   95 LYS cc_start: 0.8618 (mttt) cc_final: 0.8326 (ttmm)
REVERT: A  170 MET cc_start: 0.7991 (mmm) cc_final: 0.7590 (mmm)
REVERT: A  176 MET cc_start: 0.8164 (tpp) cc_final: 0.7903 (mmt)
REVERT: A  254 TRP cc_start: 0.8116 (t-100) cc_final: 0.7812 (t-100)
REVERT: A  356 PHE cc_start: 0.7219 (m-80) cc_final: 0.6767 (t80)
REVERT: A  381 ILE cc_start: 0.8552 (tp) cc_final: 0.8250 (tp)
REVERT: A  390 MET cc_start: 0.8152 (mmt) cc_final: 0.7403 (mmt)
  outliers start: 16
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1345
  time to fit residues: 16.8442
Evaluate side-chains
  89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 THR
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  422 TYR
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  612 SER
Chi-restraints excluded: chain A residue  615 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.177324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.118897 restraints weight = 5106.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.122239 restraints weight = 3449.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.124157 restraints weight = 2723.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   4388  Z= 0.294
  Angle     :  0.745   9.655   5974  Z= 0.362
  Chirality :  0.046   0.225    695
  Planarity :  0.004   0.043    726
  Dihedral  :  7.273  87.848    680
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 18.00 %
    Favored  : 76.64 %
  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:  0.24 (0.35), residues: 562
  helix:  1.08 (0.27), residues: 349
  sheet:  None (None), residues: 0
  loop : -1.41 (0.40), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 254 
 HIS   0.004   0.001   HIS A  54 
 PHE   0.016   0.002   PHE A 356 
 TYR   0.024   0.002   TYR A 590 
 ARG   0.007   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00204 (    2)
  link_NAG-ASN         : angle       3.14414 (    6)
  link_BETA1-4         : bond        0.00763 (    1)
  link_BETA1-4         : angle       5.74417 (    3)
  hydrogen bonds       : bond        0.05131 (  263)
  hydrogen bonds       : angle       4.69584 (  777)
  SS BOND              : bond        0.00282 (    7)
  SS BOND              : angle       1.53968 (   14)
  covalent geometry    : bond        0.00727 ( 4378)
  covalent geometry    : angle       0.72421 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8724 (mttt) cc_final: 0.8425 (ttmm)
REVERT: A  254 TRP cc_start: 0.8256 (t-100) cc_final: 0.7712 (t60)
REVERT: A  356 PHE cc_start: 0.7292 (m-80) cc_final: 0.6839 (t80)
REVERT: A  381 ILE cc_start: 0.8654 (tp) cc_final: 0.8340 (tp)
REVERT: A  390 MET cc_start: 0.8277 (mmt) cc_final: 0.7492 (mmt)
  outliers start: 22
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1298
  time to fit residues: 16.4475
Evaluate side-chains
  91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue   72 SER
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  612 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0020
   chunk 38 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9980
   chunk 37 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5766

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

Flipped N/Q/H residues before XYZ refinement:
A 365 GLN
A 520 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.213389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.163749 restraints weight = 4778.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.167318 restraints weight = 3046.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.169418 restraints weight = 2317.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4388  Z= 0.137
  Angle     :  0.637   8.496   5974  Z= 0.311
  Chirality :  0.041   0.199    695
  Planarity :  0.003   0.033    726
  Dihedral  :  7.013  81.280    680
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.87 %
    Favored  : 73.72 %
  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:  0.94 (0.36), residues: 562
  helix:  1.71 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.12 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A 520 
 PHE   0.013   0.001   PHE A 591 
 TYR   0.022   0.002   TYR A 590 
 ARG   0.007   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    2)
  link_NAG-ASN         : angle       2.85719 (    6)
  link_BETA1-4         : bond        0.00446 (    1)
  link_BETA1-4         : angle       5.32322 (    3)
  hydrogen bonds       : bond        0.04330 (  263)
  hydrogen bonds       : angle       4.20373 (  777)
  SS BOND              : bond        0.00282 (    7)
  SS BOND              : angle       2.08382 (   14)
  covalent geometry    : bond        0.00316 ( 4378)
  covalent geometry    : angle       0.61213 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 LYS cc_start: 0.8569 (mttt) cc_final: 0.8322 (ttmm)
REVERT: A  176 MET cc_start: 0.8165 (tpp) cc_final: 0.7895 (mmt)
REVERT: A  254 TRP cc_start: 0.8159 (t-100) cc_final: 0.7597 (t60)
REVERT: A  356 PHE cc_start: 0.7215 (m-80) cc_final: 0.6719 (t80)
REVERT: A  381 ILE cc_start: 0.8622 (tp) cc_final: 0.8306 (tp)
REVERT: A  390 MET cc_start: 0.8166 (mmt) cc_final: 0.7444 (mmt)
  outliers start: 14
  outliers final: 9
  residues processed: 88
  average time/residue: 0.1307
  time to fit residues: 15.2817
Evaluate side-chains
  87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 27 optimal weight:    0.6980
   chunk 20 optimal weight:    9.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.169461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.122060 restraints weight = 4666.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.118923 restraints weight = 4386.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.119712 restraints weight = 4182.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4388  Z= 0.148
  Angle     :  0.631   8.664   5974  Z= 0.306
  Chirality :  0.041   0.199    695
  Planarity :  0.004   0.031    726
  Dihedral  :  6.851  78.569    680
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.11 %
    Favored  : 73.24 %
  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:  1.12 (0.36), residues: 562
  helix:  1.84 (0.29), residues: 340
  sheet:  None (None), residues: 0
  loop : -1.04 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 254 
 HIS   0.002   0.001   HIS A  92 
 PHE   0.012   0.001   PHE A 427 
 TYR   0.025   0.002   TYR A 234 
 ARG   0.006   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00251 (    2)
  link_NAG-ASN         : angle       2.61805 (    6)
  link_BETA1-4         : bond        0.00471 (    1)
  link_BETA1-4         : angle       5.00624 (    3)
  hydrogen bonds       : bond        0.04217 (  263)
  hydrogen bonds       : angle       4.18148 (  777)
  SS BOND              : bond        0.00108 (    7)
  SS BOND              : angle       1.78999 (   14)
  covalent geometry    : bond        0.00350 ( 4378)
  covalent geometry    : angle       0.60994 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.9025 (tpp) cc_final: 0.8757 (tpp)
REVERT: A  254 TRP cc_start: 0.8185 (t-100) cc_final: 0.7736 (t-100)
REVERT: A  356 PHE cc_start: 0.7190 (m-80) cc_final: 0.6706 (t80)
REVERT: A  381 ILE cc_start: 0.8789 (tp) cc_final: 0.8456 (tp)
  outliers start: 15
  outliers final: 11
  residues processed: 89
  average time/residue: 0.1291
  time to fit residues: 15.2974
Evaluate side-chains
  90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  594 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0770
   chunk 39 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 41 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.163823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.119017 restraints weight = 4800.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.116720 restraints weight = 4033.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.118430 restraints weight = 3851.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4388  Z= 0.142
  Angle     :  0.634   8.497   5974  Z= 0.308
  Chirality :  0.041   0.194    695
  Planarity :  0.003   0.029    726
  Dihedral  :  6.734  77.098    680
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.36 %
    Favored  : 72.75 %
  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:  1.22 (0.37), residues: 562
  helix:  1.89 (0.29), residues: 340
  sheet:  None (None), residues: 0
  loop : -0.93 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 254 
 HIS   0.008   0.001   HIS A  92 
 PHE   0.011   0.001   PHE A 591 
 TYR   0.023   0.002   TYR A 590 
 ARG   0.007   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       2.52881 (    6)
  link_BETA1-4         : bond        0.00580 (    1)
  link_BETA1-4         : angle       4.78276 (    3)
  hydrogen bonds       : bond        0.04107 (  263)
  hydrogen bonds       : angle       4.10842 (  777)
  SS BOND              : bond        0.00105 (    7)
  SS BOND              : angle       1.61444 (   14)
  covalent geometry    : bond        0.00338 ( 4378)
  covalent geometry    : angle       0.61598 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8854 (tpp) cc_final: 0.8613 (tpp)
REVERT: A  170 MET cc_start: 0.7642 (mmm) cc_final: 0.7333 (mmm)
REVERT: A  246 ARG cc_start: 0.8073 (mpt-90) cc_final: 0.7192 (ptt-90)
REVERT: A  254 TRP cc_start: 0.8212 (t-100) cc_final: 0.7703 (t-100)
REVERT: A  356 PHE cc_start: 0.7172 (m-80) cc_final: 0.6671 (t80)
REVERT: A  381 ILE cc_start: 0.8532 (tp) cc_final: 0.8204 (tp)
  outliers start: 16
  outliers final: 13
  residues processed: 86
  average time/residue: 0.1417
  time to fit residues: 16.0513
Evaluate side-chains
  88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  422 TYR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  612 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.165770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.122028 restraints weight = 4849.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.117635 restraints weight = 4364.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.119489 restraints weight = 4704.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4388  Z= 0.138
  Angle     :  0.626   8.231   5974  Z= 0.306
  Chirality :  0.042   0.199    695
  Planarity :  0.003   0.028    726
  Dihedral  :  6.636  76.320    680
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.09 %
    Favored  : 72.26 %
  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:  1.14 (0.36), residues: 562
  helix:  1.77 (0.28), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.95 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 254 
 HIS   0.007   0.001   HIS A  92 
 PHE   0.010   0.001   PHE A 591 
 TYR   0.023   0.002   TYR A 590 
 ARG   0.004   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00260 (    2)
  link_NAG-ASN         : angle       2.45961 (    6)
  link_BETA1-4         : bond        0.00576 (    1)
  link_BETA1-4         : angle       4.57598 (    3)
  hydrogen bonds       : bond        0.04069 (  263)
  hydrogen bonds       : angle       4.11484 (  777)
  SS BOND              : bond        0.00104 (    7)
  SS BOND              : angle       1.50407 (   14)
  covalent geometry    : bond        0.00327 ( 4378)
  covalent geometry    : angle       0.60928 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8880 (tpp) cc_final: 0.8676 (tpp)
REVERT: A  170 MET cc_start: 0.7611 (mmm) cc_final: 0.7252 (mmm)
REVERT: A  245 ILE cc_start: 0.8464 (mm) cc_final: 0.8242 (mm)
REVERT: A  246 ARG cc_start: 0.8123 (mpt-90) cc_final: 0.7221 (ptt-90)
REVERT: A  254 TRP cc_start: 0.8258 (t-100) cc_final: 0.7646 (t60)
REVERT: A  356 PHE cc_start: 0.7199 (m-80) cc_final: 0.6648 (t80)
REVERT: A  381 ILE cc_start: 0.8557 (tp) cc_final: 0.8226 (tp)
  outliers start: 15
  outliers final: 14
  residues processed: 83
  average time/residue: 0.1716
  time to fit residues: 19.2794
Evaluate side-chains
  88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  422 TYR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  612 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 18 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.164568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.119424 restraints weight = 4736.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.116762 restraints weight = 4018.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.117439 restraints weight = 4081.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4388  Z= 0.141
  Angle     :  0.637   8.488   5974  Z= 0.308
  Chirality :  0.043   0.267    695
  Planarity :  0.003   0.028    726
  Dihedral  :  6.550  77.004    680
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.82 %
    Favored  : 72.02 %
  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:  1.21 (0.36), residues: 562
  helix:  1.82 (0.28), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.91 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 254 
 HIS   0.005   0.001   HIS A  92 
 PHE   0.014   0.001   PHE A 427 
 TYR   0.023   0.001   TYR A 590 
 ARG   0.004   0.000   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    2)
  link_NAG-ASN         : angle       2.41473 (    6)
  link_BETA1-4         : bond        0.00607 (    1)
  link_BETA1-4         : angle       4.33692 (    3)
  hydrogen bonds       : bond        0.04043 (  263)
  hydrogen bonds       : angle       4.12111 (  777)
  SS BOND              : bond        0.00082 (    7)
  SS BOND              : angle       1.41530 (   14)
  covalent geometry    : bond        0.00337 ( 4378)
  covalent geometry    : angle       0.62268 ( 5951)

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

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

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1124 Ramachandran restraints generated.
    562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.8872 (tpp) cc_final: 0.8671 (tpp)
REVERT: A  170 MET cc_start: 0.7629 (mmm) cc_final: 0.7265 (mmm)
REVERT: A  245 ILE cc_start: 0.8497 (mm) cc_final: 0.8262 (mm)
REVERT: A  246 ARG cc_start: 0.8154 (mpt-90) cc_final: 0.7280 (ptt-90)
REVERT: A  254 TRP cc_start: 0.8290 (t-100) cc_final: 0.7665 (t60)
REVERT: A  356 PHE cc_start: 0.7232 (m-80) cc_final: 0.6709 (t80)
REVERT: A  381 ILE cc_start: 0.8547 (tp) cc_final: 0.8219 (tp)
  outliers start: 13
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1369
  time to fit residues: 15.1650
Evaluate side-chains
  87 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  422 TYR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  612 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 48 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0270
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.167526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.122360 restraints weight = 4811.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.120072 restraints weight = 4035.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.121231 restraints weight = 3835.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4388  Z= 0.125
  Angle     :  0.611   7.934   5974  Z= 0.297
  Chirality :  0.042   0.270    695
  Planarity :  0.003   0.029    726
  Dihedral  :  6.398  75.182    680
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 24.57 %
    Favored  : 72.26 %
  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 (0.37), residues: 562
  helix:  1.95 (0.29), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 254 
 HIS   0.006   0.001   HIS A  92 
 PHE   0.012   0.001   PHE A 427 
 TYR   0.025   0.001   TYR A 590 
 ARG   0.009   0.001   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00269 (    2)
  link_NAG-ASN         : angle       2.37894 (    6)
  link_BETA1-4         : bond        0.00601 (    1)
  link_BETA1-4         : angle       4.14961 (    3)
  hydrogen bonds       : bond        0.03815 (  263)
  hydrogen bonds       : angle       4.03698 (  777)
  SS BOND              : bond        0.00092 (    7)
  SS BOND              : angle       1.35839 (   14)
  covalent geometry    : bond        0.00287 ( 4378)
  covalent geometry    : angle       0.59618 ( 5951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.72 seconds
wall clock time: 30 minutes 47.69 seconds (1847.69 seconds total)