Starting phenix.real_space_refine
on Thu Jul 24 15:09:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x95_33067/07_2025/7x95_33067_trim.cif"
  }
  resolution = 3.9
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2137      2.51       5
     N     557      2.21       5
     O     637      1.98       5
     H    3176      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6522
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3043
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 3043
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
    Chain: "H"
      Number of atoms: 1887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1887
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1564
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    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
  Time building chain proxies: 3.47, per 1000 atoms: 0.53
  Number of scatterers: 6522
  At special positions: 0
  Unit cell: (90.361, 87.874, 66.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     O     637      8.00
     N     557      7.00
     C    2137      6.00
     H    3176      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " 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 B   1 " - " ASN A 343 "
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 640.0 milliseconds
  

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 7 sheets defined
      9.8% alpha, 26.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
      removed outlier: 3.591A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.089A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 4.787A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 408
      removed outlier: 4.409A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 405 through 408'
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.007A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.203A  pdb=" N   GLU L  84 " --> pdb=" O   SER L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.500A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 433 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 8
    Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.629A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49
      removed outlier: 5.563A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    228 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: 2.05

  Time building geometry restraints manager: 1.96 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3176
        1.03 -     1.23: 10
        1.23 -     1.42: 1526
        1.42 -     1.62: 1883
        1.62 -     1.81: 18
  Bond restraints: 6613
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.21e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C3  NAG B   2 "
       pdb=" O3  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.01e+00
  bond pdb=" C3  NAG B   1 "
       pdb=" O3  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.78e-01
  ... (remaining 6608 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 11207
        1.07 -     2.13: 592
        2.13 -     3.20: 33
        3.20 -     4.26: 11
        4.26 -     5.33: 1
  Bond angle restraints: 11844
  Sorted by residual:
  angle pdb=" C   LEU A 518 "
        pdb=" CA  LEU A 518 "
        pdb=" CB  LEU A 518 "
      ideal   model   delta    sigma   weight residual
     116.54  112.37    4.17 1.15e+00 7.56e-01 1.31e+01
  angle pdb=" N   GLY L  15 "
        pdb=" CA  GLY L  15 "
        pdb=" C   GLY L  15 "
      ideal   model   delta    sigma   weight residual
     113.18  118.51   -5.33 2.37e+00 1.78e-01 5.06e+00
  angle pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
        pdb=" N   GLY H   9 "
      ideal   model   delta    sigma   weight residual
     114.85  116.83   -1.98 9.50e-01 1.11e+00 4.32e+00
  angle pdb=" CA  GLY H   8 "
        pdb=" C   GLY H   8 "
        pdb=" O   GLY H   8 "
      ideal   model   delta    sigma   weight residual
     122.25  120.57    1.68 9.90e-01 1.02e+00 2.87e+00
  angle pdb=" CA  LEU A 518 "
        pdb=" C   LEU A 518 "
        pdb=" N   HIS A 519 "
      ideal   model   delta    sigma   weight residual
     119.52  118.19    1.33 7.90e-01 1.60e+00 2.85e+00
  ... (remaining 11839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 2909
       17.50 -    35.00: 216
       35.00 -    52.50: 80
       52.50 -    70.00: 16
       70.00 -    87.50: 2
  Dihedral angle restraints: 3223
    sinusoidal: 1702
      harmonic: 1521
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.50  -41.50     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.62   36.38     1      1.00e+01 1.00e-02 1.87e+01
  dihedral pdb=" CA  LEU L  96 "
           pdb=" C   LEU L  96 "
           pdb=" N   PHE L  97 "
           pdb=" CA  PHE L  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.73  -18.27     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 275
       0.026 -    0.053: 153
       0.053 -    0.079: 38
       0.079 -    0.106: 23
       0.106 -    0.132: 16
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL L  59 "
            pdb=" N   VAL L  59 "
            pdb=" C   VAL L  59 "
            pdb=" CB  VAL L  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL H 122 "
            pdb=" N   VAL H 122 "
            pdb=" C   VAL H 122 "
            pdb=" CB  VAL H 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 502 not shown)

  Planarity restraints: 1002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR L  13 "    0.040 5.00e-02 4.00e+02   6.03e-02 5.81e+00
        pdb=" N   PRO L  14 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO L  14 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO L  14 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L   7 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO L   8 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.06e+00
        pdb=" N   PRO A 463 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.014 5.00e-02 4.00e+02
  ... (remaining 999 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 508
        2.20 -     2.80: 13089
        2.80 -     3.40: 16606
        3.40 -     4.00: 22671
        4.00 -     4.60: 33900
  Nonbonded interactions: 86774
  Sorted by model distance:
  nonbonded pdb=" H   GLN H 100 "
            pdb=" OD2 ASP H 114 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   PHE H  29 "
            pdb="HH22 ARG H  72 "
     model   vdw
     1.623 2.450
  nonbonded pdb="HH22 ARG H  67 "
            pdb=" OD2 ASP H  90 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OD1 ASP L  86 "
            pdb=" H   THR L 104 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" HZ2 LYS A 417 "
            pdb=" OH  TYR H 109 "
     model   vdw
     1.681 2.450
  ... (remaining 86769 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:             0.280
  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:             0.110
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.890
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
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      :  0.003   0.035   3445  Z= 0.125
  Angle     :  0.508   5.329   4694  Z= 0.268
  Chirality :  0.042   0.132    505
  Planarity :  0.004   0.060    598
  Dihedral  : 13.803  87.503   1235
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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: -1.00 (0.42), residues: 421
  helix: -1.95 (1.84), residues: 12
  sheet:  0.33 (0.45), residues: 137
  loop : -1.18 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  36 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.008   0.001   PHE A 400 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       1.39264 (    3)
  link_BETA1-4         : bond        0.00955 (    1)
  link_BETA1-4         : angle       2.14677 (    3)
  hydrogen bonds       : bond        0.11704 (   93)
  hydrogen bonds       : angle       6.24693 (  228)
  SS BOND              : bond        0.00200 (    6)
  SS BOND              : angle       0.95016 (   12)
  covalent geometry    : bond        0.00270 ( 3437)
  covalent geometry    : angle       0.50263 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ASN cc_start: 0.8532 (p0) cc_final: 0.8309 (p0)
REVERT: H   35 HIS cc_start: 0.6588 (m170) cc_final: 0.6326 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.4475
  time to fit residues: 43.1646
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0870
   chunk 17 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
L  28 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.044465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.036203 restraints weight = 53045.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.038421 restraints weight = 20501.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.039981 restraints weight = 10650.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3445  Z= 0.153
  Angle     :  0.554   5.138   4694  Z= 0.287
  Chirality :  0.041   0.137    505
  Planarity :  0.004   0.063    598
  Dihedral  :  6.755  56.041    514
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  8.08 %
    Favored  : 90.81 %
  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: -1.08 (0.41), residues: 421
  helix: -1.86 (1.88), residues: 12
  sheet:  0.21 (0.45), residues: 138
  loop : -1.21 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  98 
 HIS   0.001   0.000   HIS L  39 
 PHE   0.005   0.001   PHE A 400 
 TYR   0.007   0.001   TYR A 453 
 ARG   0.002   0.000   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00129 (    1)
  link_NAG-ASN         : angle       1.73546 (    3)
  link_BETA1-4         : bond        0.00505 (    1)
  link_BETA1-4         : angle       1.48386 (    3)
  hydrogen bonds       : bond        0.03457 (   93)
  hydrogen bonds       : angle       5.82094 (  228)
  SS BOND              : bond        0.00803 (    6)
  SS BOND              : angle       1.67042 (   12)
  covalent geometry    : bond        0.00340 ( 3437)
  covalent geometry    : angle       0.54566 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9392 (mmmm) cc_final: 0.8880 (ttmm)
REVERT: A  465 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6862 (tm-30)
REVERT: H   34 MET cc_start: 0.9248 (mmm) cc_final: 0.8798 (mmm)
REVERT: H   35 HIS cc_start: 0.9284 (m170) cc_final: 0.7860 (m170)
  outliers start: 4
  outliers final: 3
  residues processed: 63
  average time/residue: 0.3470
  time to fit residues: 26.4609
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 8 optimal weight:    8.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   overall best weight:    4.7588

-------------------------------------------------------------------------------
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 = 0.2918 r_free = 0.2918 target = 0.043181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.035093 restraints weight = 54146.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.037265 restraints weight = 20819.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.038760 restraints weight = 10780.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3445  Z= 0.195
  Angle     :  0.569   4.865   4694  Z= 0.295
  Chirality :  0.041   0.140    505
  Planarity :  0.004   0.064    598
  Dihedral  :  6.337  45.565    514
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.86 %
    Favored  : 88.58 %
  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: -1.13 (0.41), residues: 421
  helix: -1.65 (1.97), residues: 12
  sheet:  0.10 (0.45), residues: 136
  loop : -1.21 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  36 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.006   0.001   PHE A 515 
 TYR   0.010   0.001   TYR L  88 
 ARG   0.001   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00293 (    1)
  link_NAG-ASN         : angle       1.83647 (    3)
  link_BETA1-4         : bond        0.00078 (    1)
  link_BETA1-4         : angle       1.23381 (    3)
  hydrogen bonds       : bond        0.03351 (   93)
  hydrogen bonds       : angle       5.73075 (  228)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       1.31857 (   12)
  covalent geometry    : bond        0.00424 ( 3437)
  covalent geometry    : angle       0.56315 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9412 (mmmm) cc_final: 0.8974 (ttmm)
REVERT: A  465 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6988 (tm-30)
REVERT: H   34 MET cc_start: 0.9288 (mmm) cc_final: 0.8820 (mmm)
REVERT: L   96 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9129 (pp)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.4224
  time to fit residues: 28.6762
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.2932 r_free = 0.2932 target = 0.043621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.035376 restraints weight = 55755.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.037577 restraints weight = 21349.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.039113 restraints weight = 11107.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3445  Z= 0.116
  Angle     :  0.550   5.813   4694  Z= 0.281
  Chirality :  0.042   0.140    505
  Planarity :  0.004   0.062    598
  Dihedral  :  5.677  43.412    514
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.86 %
    Favored  : 88.30 %
  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: -0.97 (0.41), residues: 421
  helix: -1.59 (2.01), residues: 12
  sheet:  0.36 (0.47), residues: 133
  loop : -1.17 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.001   0.001   HIS H  35 
 PHE   0.007   0.001   PHE A 400 
 TYR   0.006   0.001   TYR A 453 
 ARG   0.001   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00003 (    1)
  link_NAG-ASN         : angle       1.34233 (    3)
  link_BETA1-4         : bond        0.00380 (    1)
  link_BETA1-4         : angle       1.11943 (    3)
  hydrogen bonds       : bond        0.03173 (   93)
  hydrogen bonds       : angle       5.55616 (  228)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       1.80518 (   12)
  covalent geometry    : bond        0.00272 ( 3437)
  covalent geometry    : angle       0.54113 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9026 (ttmm)
REVERT: A  465 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7025 (tm-30)
REVERT: H   34 MET cc_start: 0.9240 (mmm) cc_final: 0.8726 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 57
  average time/residue: 0.3347
  time to fit residues: 23.4529
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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 = 0.2883 r_free = 0.2883 target = 0.041658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.033663 restraints weight = 55774.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.035739 restraints weight = 21409.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.037187 restraints weight = 11162.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3445  Z= 0.222
  Angle     :  0.585   5.398   4694  Z= 0.303
  Chirality :  0.040   0.139    505
  Planarity :  0.004   0.063    598
  Dihedral  :  5.583  44.503    514
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.81 %
    Favored  : 86.07 %
  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: -1.17 (0.40), residues: 421
  helix: -1.71 (1.90), residues: 12
  sheet:  0.21 (0.46), residues: 133
  loop : -1.30 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L  39 
 PHE   0.007   0.001   PHE H 107 
 TYR   0.009   0.001   TYR A 365 
 ARG   0.001   0.000   ARG L  51 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00490 (    1)
  link_NAG-ASN         : angle       1.86374 (    3)
  link_BETA1-4         : bond        0.00105 (    1)
  link_BETA1-4         : angle       1.08039 (    3)
  hydrogen bonds       : bond        0.03402 (   93)
  hydrogen bonds       : angle       5.65814 (  228)
  SS BOND              : bond        0.00869 (    6)
  SS BOND              : angle       1.86406 (   12)
  covalent geometry    : bond        0.00475 ( 3437)
  covalent geometry    : angle       0.57594 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9458 (mmmm) cc_final: 0.9111 (ttmm)
REVERT: A  465 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7083 (tm-30)
REVERT: L   96 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9154 (pp)
  outliers start: 4
  outliers final: 1
  residues processed: 50
  average time/residue: 0.4300
  time to fit residues: 26.5678
Evaluate side-chains
  51 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.042270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.034233 restraints weight = 55320.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.036309 restraints weight = 21335.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.037801 restraints weight = 11197.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3445  Z= 0.134
  Angle     :  0.547   6.328   4694  Z= 0.281
  Chirality :  0.041   0.142    505
  Planarity :  0.004   0.060    598
  Dihedral  :  5.253  42.527    514
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.48 %
    Favored  : 84.40 %
  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: -1.02 (0.40), residues: 421
  helix: -1.50 (1.98), residues: 12
  sheet:  0.29 (0.46), residues: 133
  loop : -1.18 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.001   0.001   HIS H  35 
 PHE   0.014   0.001   PHE A 456 
 TYR   0.005   0.001   TYR A 365 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       1.35255 (    3)
  link_BETA1-4         : bond        0.00247 (    1)
  link_BETA1-4         : angle       0.95897 (    3)
  hydrogen bonds       : bond        0.03157 (   93)
  hydrogen bonds       : angle       5.52863 (  228)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       1.50478 (   12)
  covalent geometry    : bond        0.00305 ( 3437)
  covalent geometry    : angle       0.54077 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9454 (mmmm) cc_final: 0.9073 (ttmm)
REVERT: A  465 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7050 (tm-30)
REVERT: L   86 ASP cc_start: 0.7842 (p0) cc_final: 0.7558 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 55
  average time/residue: 0.4070
  time to fit residues: 26.9418
Evaluate side-chains
  56 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.2871 r_free = 0.2871 target = 0.040917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.033045 restraints weight = 56442.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.035048 restraints weight = 21593.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.036456 restraints weight = 11320.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3445  Z= 0.207
  Angle     :  0.566   4.646   4694  Z= 0.295
  Chirality :  0.041   0.141    505
  Planarity :  0.004   0.062    598
  Dihedral  :  5.315  43.597    514
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.93 %
    Favored  : 84.96 %
  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: -1.24 (0.39), residues: 421
  helix: -2.14 (1.31), residues: 18
  sheet:  0.25 (0.44), residues: 132
  loop : -1.35 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L  39 
 PHE   0.014   0.001   PHE A 456 
 TYR   0.008   0.001   TYR A 365 
 ARG   0.002   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00386 (    1)
  link_NAG-ASN         : angle       1.75738 (    3)
  link_BETA1-4         : bond        0.00067 (    1)
  link_BETA1-4         : angle       0.91603 (    3)
  hydrogen bonds       : bond        0.03360 (   93)
  hydrogen bonds       : angle       5.64178 (  228)
  SS BOND              : bond        0.00282 (    6)
  SS BOND              : angle       1.37271 (   12)
  covalent geometry    : bond        0.00447 ( 3437)
  covalent geometry    : angle       0.56070 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9492 (mmmm) cc_final: 0.9157 (ttmm)
REVERT: A  465 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6759 (tm-30)
REVERT: L   96 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9165 (pp)
  outliers start: 4
  outliers final: 3
  residues processed: 52
  average time/residue: 0.3876
  time to fit residues: 24.3438
Evaluate side-chains
  54 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 34 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 474 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 = 0.2859 r_free = 0.2859 target = 0.040419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.032723 restraints weight = 57286.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.034697 restraints weight = 22251.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.036075 restraints weight = 11716.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3445  Z= 0.234
  Angle     :  0.619   9.956   4694  Z= 0.318
  Chirality :  0.041   0.139    505
  Planarity :  0.004   0.061    598
  Dihedral  :  5.367  42.960    514
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 15.60 %
    Favored  : 83.29 %
  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 (0.39), residues: 421
  helix: -2.70 (1.16), residues: 18
  sheet:  0.30 (0.45), residues: 132
  loop : -1.43 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS L  39 
 PHE   0.012   0.001   PHE A 456 
 TYR   0.008   0.001   TYR A 365 
 ARG   0.002   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00437 (    1)
  link_NAG-ASN         : angle       1.75332 (    3)
  link_BETA1-4         : bond        0.00088 (    1)
  link_BETA1-4         : angle       1.08659 (    3)
  hydrogen bonds       : bond        0.03462 (   93)
  hydrogen bonds       : angle       5.74024 (  228)
  SS BOND              : bond        0.00326 (    6)
  SS BOND              : angle       1.30626 (   12)
  covalent geometry    : bond        0.00500 ( 3437)
  covalent geometry    : angle       0.61466 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9481 (mmmm) cc_final: 0.9151 (ttmm)
REVERT: H   83 MET cc_start: 0.9460 (mmm) cc_final: 0.9171 (tpp)
REVERT: L   96 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9188 (pp)
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.3733
  time to fit residues: 22.5724
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain L residue   28 ASN
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:    0.3980
   chunk 35 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.041849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.033634 restraints weight = 55585.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.035737 restraints weight = 21275.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.037214 restraints weight = 11204.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3445  Z= 0.104
  Angle     :  0.575   6.665   4694  Z= 0.291
  Chirality :  0.043   0.158    505
  Planarity :  0.004   0.061    598
  Dihedral  :  4.915  39.929    514
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 15.60 %
    Favored  : 83.84 %
  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: -1.10 (0.40), residues: 421
  helix: -2.35 (1.32), residues: 18
  sheet:  0.31 (0.45), residues: 132
  loop : -1.20 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  36 
 HIS   0.002   0.001   HIS L  39 
 PHE   0.015   0.001   PHE A 456 
 TYR   0.006   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00147 (    1)
  link_NAG-ASN         : angle       1.12259 (    3)
  link_BETA1-4         : bond        0.00648 (    1)
  link_BETA1-4         : angle       1.23210 (    3)
  hydrogen bonds       : bond        0.03157 (   93)
  hydrogen bonds       : angle       5.69683 (  228)
  SS BOND              : bond        0.00260 (    6)
  SS BOND              : angle       1.31972 (   12)
  covalent geometry    : bond        0.00255 ( 3437)
  covalent geometry    : angle       0.57056 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9473 (mmmm) cc_final: 0.9147 (ttmm)
REVERT: A  465 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: L   86 ASP cc_start: 0.7903 (p0) cc_final: 0.7629 (p0)
  outliers start: 2
  outliers final: 2
  residues processed: 56
  average time/residue: 0.3318
  time to fit residues: 22.9929
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    5.9990
   chunk 18 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    3.8386

-------------------------------------------------------------------------------
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 = 0.2887 r_free = 0.2887 target = 0.041458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.033596 restraints weight = 56813.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.035650 restraints weight = 21617.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.037102 restraints weight = 11281.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3445  Z= 0.160
  Angle     :  0.579   5.490   4694  Z= 0.299
  Chirality :  0.041   0.150    505
  Planarity :  0.004   0.061    598
  Dihedral  :  5.029  40.368    514
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 15.88 %
    Favored  : 83.29 %
  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: -1.16 (0.40), residues: 421
  helix: -2.49 (1.33), residues: 18
  sheet:  0.30 (0.44), residues: 132
  loop : -1.25 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H 116 
 HIS   0.002   0.000   HIS L  39 
 PHE   0.013   0.001   PHE A 456 
 TYR   0.006   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       1.47705 (    3)
  link_BETA1-4         : bond        0.00250 (    1)
  link_BETA1-4         : angle       1.07060 (    3)
  hydrogen bonds       : bond        0.03203 (   93)
  hydrogen bonds       : angle       5.69083 (  228)
  SS BOND              : bond        0.00363 (    6)
  SS BOND              : angle       1.50530 (   12)
  covalent geometry    : bond        0.00355 ( 3437)
  covalent geometry    : angle       0.57330 ( 4676)

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

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

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  842 Ramachandran restraints generated.
    421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9179 (ttmm)
REVERT: A  465 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7298 (tm-30)
REVERT: H   83 MET cc_start: 0.9476 (mmm) cc_final: 0.9187 (tpp)
REVERT: L   96 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9159 (pp)
  outliers start: 3
  outliers final: 2
  residues processed: 50
  average time/residue: 0.3307
  time to fit residues: 20.8091
Evaluate side-chains
  52 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain L residue   96 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.2908 r_free = 0.2908 target = 0.042192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.034066 restraints weight = 55849.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.036194 restraints weight = 21248.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.037694 restraints weight = 11074.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3445  Z= 0.106
  Angle     :  0.559   5.385   4694  Z= 0.285
  Chirality :  0.042   0.146    505
  Planarity :  0.004   0.061    598
  Dihedral  :  4.752  37.444    514
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 15.88 %
    Favored  : 83.57 %
  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: -1.02 (0.41), residues: 421
  helix: -2.57 (1.31), residues: 18
  sheet:  0.30 (0.45), residues: 135
  loop : -1.09 (0.38), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L  98 
 HIS   0.002   0.001   HIS L  39 
 PHE   0.014   0.001   PHE A 456 
 TYR   0.005   0.001   TYR A 421 
 ARG   0.002   0.000   ARG A 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00078 (    1)
  link_NAG-ASN         : angle       1.12789 (    3)
  link_BETA1-4         : bond        0.00525 (    1)
  link_BETA1-4         : angle       1.16891 (    3)
  hydrogen bonds       : bond        0.03023 (   93)
  hydrogen bonds       : angle       5.48528 (  228)
  SS BOND              : bond        0.00314 (    6)
  SS BOND              : angle       1.39223 (   12)
  covalent geometry    : bond        0.00252 ( 3437)
  covalent geometry    : angle       0.55404 ( 4676)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2909.46 seconds
wall clock time: 51 minutes 11.63 seconds (3071.63 seconds total)