Starting phenix.real_space_refine
on Fri May  9 21:59:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dt3_27690/05_2025/8dt3_27690_neut.cif"
  }
  resolution = 3.3
  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: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2416      2.51       5
     N     636      2.21       5
     O     751      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3821
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 2005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 2005
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 13, 'TRANS': 239}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 927
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 851
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
    Chain: "T"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.33, per 1000 atoms: 0.87
  Number of scatterers: 3821
  At special positions: 0
  Unit cell: (59.4, 97.2, 104.76, 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      18     16.00
     O     751      8.00
     N     636      7.00
     C    2416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - 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 T   1 " - " NAG T   2 "
    BETA1-6
      " NAG T   1 " - " FUC T   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG T   1 " - " ASN C 343 "
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 452.1 milliseconds
  

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  890

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      12.4% alpha, 34.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 3.936A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   TYR C 369 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 390
      removed outlier: 3.794A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.296A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
      removed outlier: 3.783A  pdb=" N   ASN C 422 " --> pdb=" O   ILE C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.925A  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
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.547A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.047A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'C' and resid 538 through 543
      removed outlier: 5.710A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLY C 566 " --> pdb=" O   ASP C 574 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.218A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   TRP H  33 " --> pdb=" O   GLY H  99 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   MET H  34 " --> pdb=" O   GLN H  50 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.218A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 111 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   TRP H 111 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 109 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13
      removed outlier: 6.924A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    291 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: 1.03

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1220
        1.35 -     1.47: 1054
        1.47 -     1.60: 1612
        1.60 -     1.72: 0
        1.72 -     1.85: 22
  Bond restraints: 3908
  Sorted by residual:
  bond pdb=" C1  FUC T   3 "
       pdb=" C2  FUC T   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.576 -0.048 2.00e-02 2.50e+03 5.81e+00
  bond pdb=" N   ASP H  57 "
       pdb=" CA  ASP H  57 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.28e-02 6.10e+03 5.58e+00
  bond pdb=" C2  FUC T   3 "
       pdb=" C3  FUC T   3 "
    ideal  model  delta    sigma   weight residual
    1.526  1.554 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C   ALA C 520 "
       pdb=" N   PRO C 521 "
    ideal  model  delta    sigma   weight residual
    1.330  1.346 -0.016 1.19e-02 7.06e+03 1.75e+00
  bond pdb=" C1  NAG T   2 "
       pdb=" O5  NAG T   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  ... (remaining 3903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 5120
        1.59 -     3.18: 141
        3.18 -     4.78: 31
        4.78 -     6.37: 7
        6.37 -     7.96: 2
  Bond angle restraints: 5301
  Sorted by residual:
  angle pdb=" C   TYR L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" CA  CYS C 432 "
        pdb=" CB  CYS C 432 "
        pdb=" SG  CYS C 432 "
      ideal   model   delta    sigma   weight residual
     114.40  122.36   -7.96 2.30e+00 1.89e-01 1.20e+01
  angle pdb=" C   GLY C 431 "
        pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
      ideal   model   delta    sigma   weight residual
     122.10  116.63    5.47 1.66e+00 3.63e-01 1.09e+01
  angle pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
        pdb=" O   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     122.65  118.60    4.05 1.28e+00 6.10e-01 1.00e+01
  angle pdb=" N   GLY C 431 "
        pdb=" CA  GLY C 431 "
        pdb=" C   GLY C 431 "
      ideal   model   delta    sigma   weight residual
     112.58  106.99    5.59 1.80e+00 3.09e-01 9.63e+00
  ... (remaining 5296 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.93: 2212
       23.93 -    47.87: 93
       47.87 -    71.80: 21
       71.80 -    95.73: 13
       95.73 -   119.67: 9
  Dihedral angle restraints: 2348
    sinusoidal: 950
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.63   55.37     1      1.00e+01 1.00e-02 4.14e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.59   46.41     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.16   38.84     1      1.00e+01 1.00e-02 2.12e+01
  ... (remaining 2345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 358
       0.032 -    0.064: 142
       0.064 -    0.095: 47
       0.095 -    0.127: 34
       0.127 -    0.159: 6
  Chirality restraints: 587
  Sorted by residual:
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.31e-01
  chirality pdb=" C5  NAG T   1 "
            pdb=" C4  NAG T   1 "
            pdb=" C6  NAG T   1 "
            pdb=" O5  NAG T   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.56    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE L  76 "
            pdb=" N   ILE L  76 "
            pdb=" C   ILE L  76 "
            pdb=" CB  ILE L  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 584 not shown)

  Planarity restraints: 680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  40 "   -0.043 5.00e-02 4.00e+02   6.48e-02 6.73e+00
        pdb=" N   PRO H  41 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 369 "   -0.014 2.00e-02 2.50e+03   1.01e-02 2.06e+00
        pdb=" CG  TYR C 369 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 369 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 369 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 369 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 369 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 369 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 369 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L  54 "   -0.098 9.50e-02 1.11e+02   4.40e-02 1.51e+00
        pdb=" NE  ARG L  54 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG L  54 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG L  54 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG L  54 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 677 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 104
        2.68 -     3.24: 3777
        3.24 -     3.79: 5799
        3.79 -     4.35: 7951
        4.35 -     4.90: 13135
  Nonbonded interactions: 30766
  Sorted by model distance:
  nonbonded pdb=" O   SER L  31 "
            pdb=" OH  TYR L  72 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OG  SER C 469 "
            pdb=" OE1 GLU C 471 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER C 530 "
            pdb=" OE1 GLN C 580 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NE2 HIS L  56 "
            pdb=" O3  FUC T   3 "
     model   vdw
     2.262 3.120
  ... (remaining 30761 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.780
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
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      :  0.004   0.048   3917  Z= 0.174
  Angle     :  0.706  10.039   5322  Z= 0.366
  Chirality :  0.045   0.159    587
  Planarity :  0.004   0.065    679
  Dihedral  : 17.521 119.666   1440
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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: -0.65 (0.40), residues: 477
  helix: -3.69 (0.56), residues: 34
  sheet:  0.93 (0.41), residues: 177
  loop : -0.95 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.013   0.001   PHE C 392 
 TYR   0.025   0.002   TYR C 369 
 ARG   0.010   0.001   ARG L  54 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    1)
  link_NAG-ASN         : angle       8.33856 (    3)
  link_BETA1-4         : bond        0.01083 (    1)
  link_BETA1-4         : angle       2.58524 (    3)
  hydrogen bonds       : bond        0.13971 (  123)
  hydrogen bonds       : angle       7.40924 (  291)
  link_BETA1-6         : bond        0.00687 (    1)
  link_BETA1-6         : angle       3.06589 (    3)
  SS BOND              : bond        0.00691 (    6)
  SS BOND              : angle       2.03373 (   12)
  covalent geometry    : bond        0.00371 ( 3908)
  covalent geometry    : angle       0.66556 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.543 
Fit side-chains
REVERT: C  365 TYR cc_start: 0.5792 (p90) cc_final: 0.5403 (p90)
REVERT: H   80 TYR cc_start: 0.8183 (m-80) cc_final: 0.7937 (m-80)
REVERT: L  105 LEU cc_start: 0.9313 (mp) cc_final: 0.8676 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1559
  time to fit residues: 13.2560
Evaluate side-chains
  58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0980
   chunk 27 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.076314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.061595 restraints weight = 12848.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.82
r_work: 0.3099 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3917  Z= 0.138
  Angle     :  0.692  10.419   5322  Z= 0.338
  Chirality :  0.046   0.154    587
  Planarity :  0.004   0.041    679
  Dihedral  : 13.190 120.406    585
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  8.37 %
    Favored  : 91.39 %
  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: -0.45 (0.40), residues: 477
  helix: -3.40 (0.67), residues: 33
  sheet:  1.14 (0.42), residues: 163
  loop : -0.80 (0.39), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.012   0.001   PHE C 392 
 TYR   0.022   0.001   TYR C 369 
 ARG   0.006   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00963 (    1)
  link_NAG-ASN         : angle       9.07271 (    3)
  link_BETA1-4         : bond        0.00488 (    1)
  link_BETA1-4         : angle       1.12213 (    3)
  hydrogen bonds       : bond        0.02884 (  123)
  hydrogen bonds       : angle       5.94898 (  291)
  link_BETA1-6         : bond        0.01038 (    1)
  link_BETA1-6         : angle       1.86032 (    3)
  SS BOND              : bond        0.00623 (    6)
  SS BOND              : angle       1.69287 (   12)
  covalent geometry    : bond        0.00322 ( 3908)
  covalent geometry    : angle       0.65217 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: C  365 TYR cc_start: 0.6130 (p90) cc_final: 0.5906 (p90)
REVERT: C  406 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8666 (mm-30)
REVERT: C  563 GLN cc_start: 0.8334 (mt0) cc_final: 0.7449 (mm110)
REVERT: H   80 TYR cc_start: 0.8500 (m-80) cc_final: 0.8203 (m-80)
REVERT: L   80 GLU cc_start: 0.8890 (tt0) cc_final: 0.8662 (tt0)
REVERT: L   81 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8340 (tp-100)
REVERT: L   82 GLU cc_start: 0.8694 (pm20) cc_final: 0.8217 (pm20)
REVERT: L   87 TYR cc_start: 0.8821 (m-80) cc_final: 0.8597 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1428
  time to fit residues: 11.9630
Evaluate side-chains
  60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   34 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0020
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 37 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.5390

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.076393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.061676 restraints weight = 12808.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 3.84
r_work: 0.3106 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3917  Z= 0.130
  Angle     :  0.638  11.236   5322  Z= 0.313
  Chirality :  0.045   0.183    587
  Planarity :  0.004   0.034    679
  Dihedral  : 10.672 104.454    585
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.77 %
    Favored  : 88.04 %
  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: -0.41 (0.40), residues: 477
  helix: -3.44 (0.67), residues: 33
  sheet:  1.30 (0.43), residues: 161
  loop : -0.84 (0.38), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.009   0.001   PHE C 565 
 TYR   0.017   0.001   TYR C 369 
 ARG   0.006   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00796 (    1)
  link_NAG-ASN         : angle       9.18546 (    3)
  link_BETA1-4         : bond        0.00496 (    1)
  link_BETA1-4         : angle       1.04780 (    3)
  hydrogen bonds       : bond        0.02815 (  123)
  hydrogen bonds       : angle       5.64716 (  291)
  link_BETA1-6         : bond        0.00784 (    1)
  link_BETA1-6         : angle       1.45355 (    3)
  SS BOND              : bond        0.00607 (    6)
  SS BOND              : angle       1.53016 (   12)
  covalent geometry    : bond        0.00305 ( 3908)
  covalent geometry    : angle       0.59465 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8671 (mm) cc_final: 0.8454 (mt)
REVERT: C  365 TYR cc_start: 0.6126 (p90) cc_final: 0.5830 (p90)
REVERT: C  493 GLN cc_start: 0.8194 (mp10) cc_final: 0.7963 (mp10)
REVERT: C  563 GLN cc_start: 0.8327 (mt0) cc_final: 0.7499 (mm110)
REVERT: H   80 TYR cc_start: 0.8492 (m-80) cc_final: 0.8211 (m-80)
REVERT: L   80 GLU cc_start: 0.8774 (tt0) cc_final: 0.8275 (tt0)
REVERT: L   82 GLU cc_start: 0.8653 (pm20) cc_final: 0.8022 (pm20)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1443
  time to fit residues: 11.7894
Evaluate side-chains
  65 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.073910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.058464 restraints weight = 13012.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 3.91
r_work: 0.3037 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3917  Z= 0.237
  Angle     :  0.686   9.897   5322  Z= 0.342
  Chirality :  0.046   0.183    587
  Planarity :  0.004   0.034    679
  Dihedral  : 10.782 102.782    585
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 11.24 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.54 (0.39), residues: 477
  helix: -3.38 (0.68), residues: 34
  sheet:  1.18 (0.43), residues: 157
  loop : -0.90 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  33 
 HIS   0.005   0.001   HIS L  56 
 PHE   0.011   0.002   PHE C 392 
 TYR   0.016   0.002   TYR C 369 
 ARG   0.008   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00430 (    1)
  link_NAG-ASN         : angle       8.81304 (    3)
  link_BETA1-4         : bond        0.00222 (    1)
  link_BETA1-4         : angle       1.02082 (    3)
  hydrogen bonds       : bond        0.03073 (  123)
  hydrogen bonds       : angle       5.68767 (  291)
  link_BETA1-6         : bond        0.00403 (    1)
  link_BETA1-6         : angle       2.35666 (    3)
  SS BOND              : bond        0.00664 (    6)
  SS BOND              : angle       1.87422 (   12)
  covalent geometry    : bond        0.00545 ( 3908)
  covalent geometry    : angle       0.64580 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8760 (mm) cc_final: 0.8521 (mt)
REVERT: C  365 TYR cc_start: 0.6137 (p90) cc_final: 0.5754 (p90)
REVERT: C  493 GLN cc_start: 0.8192 (mp10) cc_final: 0.7980 (mp10)
REVERT: C  563 GLN cc_start: 0.8439 (mt0) cc_final: 0.7721 (mm110)
REVERT: H   80 TYR cc_start: 0.8625 (m-80) cc_final: 0.8397 (m-80)
REVERT: L   80 GLU cc_start: 0.8846 (tt0) cc_final: 0.8394 (tt0)
  outliers start: 9
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1296
  time to fit residues: 9.7185
Evaluate side-chains
  61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 0 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.3980
   chunk 7 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.074438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.059400 restraints weight = 13182.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 3.86
r_work: 0.3065 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3917  Z= 0.160
  Angle     :  0.652  10.508   5322  Z= 0.322
  Chirality :  0.045   0.170    587
  Planarity :  0.003   0.032    679
  Dihedral  : 10.038  94.403    585
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.96 %
    Favored  : 85.41 %
  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: -0.55 (0.39), residues: 477
  helix: -3.48 (0.63), residues: 34
  sheet:  1.18 (0.43), residues: 157
  loop : -0.89 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.011   0.001   PHE C 559 
 TYR   0.015   0.001   TYR C 369 
 ARG   0.003   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00610 (    1)
  link_NAG-ASN         : angle       9.02582 (    3)
  link_BETA1-4         : bond        0.00301 (    1)
  link_BETA1-4         : angle       1.10909 (    3)
  hydrogen bonds       : bond        0.02845 (  123)
  hydrogen bonds       : angle       5.57147 (  291)
  link_BETA1-6         : bond        0.00916 (    1)
  link_BETA1-6         : angle       2.23579 (    3)
  SS BOND              : bond        0.00621 (    6)
  SS BOND              : angle       1.85022 (   12)
  covalent geometry    : bond        0.00371 ( 3908)
  covalent geometry    : angle       0.60822 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8709 (mm) cc_final: 0.8472 (mt)
REVERT: C  559 PHE cc_start: 0.2885 (OUTLIER) cc_final: 0.1704 (m-80)
REVERT: C  563 GLN cc_start: 0.8488 (mt0) cc_final: 0.7486 (mm110)
REVERT: H   80 TYR cc_start: 0.8574 (m-80) cc_final: 0.8342 (m-80)
REVERT: L   80 GLU cc_start: 0.8824 (tt0) cc_final: 0.8351 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 62
  average time/residue: 0.1401
  time to fit residues: 11.1700
Evaluate side-chains
  66 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.074656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.059842 restraints weight = 12882.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 3.82
r_work: 0.3068 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.169
  Angle     :  0.655  10.550   5322  Z= 0.323
  Chirality :  0.045   0.177    587
  Planarity :  0.004   0.031    679
  Dihedral  :  9.611  89.749    585
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.16 %
    Favored  : 84.21 %
  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: -0.53 (0.39), residues: 477
  helix: -3.33 (0.66), residues: 34
  sheet:  1.16 (0.43), residues: 157
  loop : -0.87 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.008   0.001   PHE C 392 
 TYR   0.017   0.001   TYR C 489 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00551 (    1)
  link_NAG-ASN         : angle       9.13584 (    3)
  link_BETA1-4         : bond        0.00330 (    1)
  link_BETA1-4         : angle       1.15010 (    3)
  hydrogen bonds       : bond        0.02847 (  123)
  hydrogen bonds       : angle       5.52299 (  291)
  link_BETA1-6         : bond        0.01035 (    1)
  link_BETA1-6         : angle       2.31471 (    3)
  SS BOND              : bond        0.00607 (    6)
  SS BOND              : angle       1.81270 (   12)
  covalent geometry    : bond        0.00389 ( 3908)
  covalent geometry    : angle       0.61030 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8680 (mm) cc_final: 0.8440 (mt)
REVERT: C  563 GLN cc_start: 0.8593 (mt0) cc_final: 0.7882 (mm110)
REVERT: H   80 TYR cc_start: 0.8585 (m-80) cc_final: 0.8354 (m-80)
REVERT: L   80 GLU cc_start: 0.8796 (tt0) cc_final: 0.8356 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.1466
  time to fit residues: 11.8974
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.074490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059698 restraints weight = 12808.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 3.80
r_work: 0.3068 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.173
  Angle     :  0.681  10.522   5322  Z= 0.331
  Chirality :  0.046   0.179    587
  Planarity :  0.004   0.029    679
  Dihedral  :  9.020  82.780    585
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.59 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.49 (0.39), residues: 477
  helix: -3.10 (0.74), residues: 33
  sheet:  1.18 (0.43), residues: 157
  loop : -0.88 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.007   0.001   PHE C 392 
 TYR   0.036   0.002   TYR C 365 
 ARG   0.008   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00508 (    1)
  link_NAG-ASN         : angle       9.19529 (    3)
  link_BETA1-4         : bond        0.00338 (    1)
  link_BETA1-4         : angle       1.19835 (    3)
  hydrogen bonds       : bond        0.02881 (  123)
  hydrogen bonds       : angle       5.50695 (  291)
  link_BETA1-6         : bond        0.01320 (    1)
  link_BETA1-6         : angle       2.27541 (    3)
  SS BOND              : bond        0.00611 (    6)
  SS BOND              : angle       1.77083 (   12)
  covalent geometry    : bond        0.00398 ( 3908)
  covalent geometry    : angle       0.63807 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.8683 (mm) cc_final: 0.8446 (mt)
REVERT: C  559 PHE cc_start: 0.3409 (OUTLIER) cc_final: 0.2176 (m-80)
REVERT: C  563 GLN cc_start: 0.8283 (mt0) cc_final: 0.7438 (mm110)
REVERT: H   80 TYR cc_start: 0.8575 (m-80) cc_final: 0.8357 (m-80)
REVERT: L   80 GLU cc_start: 0.8869 (tt0) cc_final: 0.8389 (tt0)
REVERT: L   81 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8251 (tp-100)
  outliers start: 12
  outliers final: 10
  residues processed: 65
  average time/residue: 0.1483
  time to fit residues: 12.3639
Evaluate side-chains
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.074677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.059729 restraints weight = 12941.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 3.84
r_work: 0.3068 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3917  Z= 0.168
  Angle     :  0.686  10.636   5322  Z= 0.333
  Chirality :  0.046   0.177    587
  Planarity :  0.004   0.030    679
  Dihedral  :  7.823  65.204    585
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.11 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.43 (0.40), residues: 477
  helix: -3.08 (0.77), residues: 33
  sheet:  1.20 (0.44), residues: 157
  loop : -0.83 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.007   0.001   PHE C 565 
 TYR   0.028   0.002   TYR C 365 
 ARG   0.009   0.000   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00439 (    1)
  link_NAG-ASN         : angle       9.29289 (    3)
  link_BETA1-4         : bond        0.00297 (    1)
  link_BETA1-4         : angle       1.30366 (    3)
  hydrogen bonds       : bond        0.02807 (  123)
  hydrogen bonds       : angle       5.45893 (  291)
  link_BETA1-6         : bond        0.02046 (    1)
  link_BETA1-6         : angle       1.83896 (    3)
  SS BOND              : bond        0.00603 (    6)
  SS BOND              : angle       1.71761 (   12)
  covalent geometry    : bond        0.00386 ( 3908)
  covalent geometry    : angle       0.64397 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.401 
Fit side-chains
REVERT: C  358 ILE cc_start: 0.8674 (mm) cc_final: 0.8439 (mt)
REVERT: C  559 PHE cc_start: 0.3570 (OUTLIER) cc_final: 0.2375 (m-80)
REVERT: C  563 GLN cc_start: 0.8256 (mt0) cc_final: 0.7364 (mm110)
REVERT: H   80 TYR cc_start: 0.8592 (m-80) cc_final: 0.8369 (m-80)
  outliers start: 14
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1552
  time to fit residues: 13.3893
Evaluate side-chains
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  450 ASN
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.074707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.059924 restraints weight = 12925.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.81
r_work: 0.3060 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.172
  Angle     :  0.707  10.760   5322  Z= 0.344
  Chirality :  0.046   0.179    587
  Planarity :  0.004   0.031    679
  Dihedral  :  7.467  58.521    585
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.55 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.40), residues: 477
  helix: -3.26 (0.71), residues: 33
  sheet:  1.19 (0.44), residues: 157
  loop : -0.81 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.010   0.001   PHE C 562 
 TYR   0.028   0.001   TYR C 365 
 ARG   0.009   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00412 (    1)
  link_NAG-ASN         : angle       9.27858 (    3)
  link_BETA1-4         : bond        0.00273 (    1)
  link_BETA1-4         : angle       1.29848 (    3)
  hydrogen bonds       : bond        0.02846 (  123)
  hydrogen bonds       : angle       5.57355 (  291)
  link_BETA1-6         : bond        0.02354 (    1)
  link_BETA1-6         : angle       1.70580 (    3)
  SS BOND              : bond        0.00601 (    6)
  SS BOND              : angle       1.71493 (   12)
  covalent geometry    : bond        0.00396 ( 3908)
  covalent geometry    : angle       0.66607 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.462 
Fit side-chains
REVERT: C  358 ILE cc_start: 0.8672 (mm) cc_final: 0.8433 (mt)
REVERT: C  516 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: C  559 PHE cc_start: 0.2980 (OUTLIER) cc_final: 0.1583 (m-80)
REVERT: C  563 GLN cc_start: 0.8321 (mt0) cc_final: 0.7447 (mm110)
REVERT: H   80 TYR cc_start: 0.8604 (m-80) cc_final: 0.8379 (m-80)
  outliers start: 13
  outliers final: 12
  residues processed: 63
  average time/residue: 0.1404
  time to fit residues: 11.6390
Evaluate side-chains
  70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  350 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  450 ASN
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.075156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.060221 restraints weight = 12765.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.83
r_work: 0.3079 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3917  Z= 0.152
  Angle     :  0.719  10.778   5322  Z= 0.352
  Chirality :  0.045   0.173    587
  Planarity :  0.004   0.029    679
  Dihedral  :  7.008  51.606    585
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.79 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.40), residues: 477
  helix: -3.25 (0.72), residues: 33
  sheet:  1.22 (0.44), residues: 157
  loop : -0.79 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  56 
 PHE   0.010   0.001   PHE C 562 
 TYR   0.029   0.002   TYR C 369 
 ARG   0.009   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00459 (    1)
  link_NAG-ASN         : angle       9.34463 (    3)
  link_BETA1-4         : bond        0.00242 (    1)
  link_BETA1-4         : angle       1.38901 (    3)
  hydrogen bonds       : bond        0.02786 (  123)
  hydrogen bonds       : angle       5.50030 (  291)
  link_BETA1-6         : bond        0.02875 (    1)
  link_BETA1-6         : angle       1.91373 (    3)
  SS BOND              : bond        0.00593 (    6)
  SS BOND              : angle       1.60244 (   12)
  covalent geometry    : bond        0.00349 ( 3908)
  covalent geometry    : angle       0.67870 ( 5301)

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

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

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  954 Ramachandran restraints generated.
    477 Oldfield, 0 Emsley, 477 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.553 
Fit side-chains
REVERT: C  358 ILE cc_start: 0.8688 (mm) cc_final: 0.8461 (mt)
REVERT: C  559 PHE cc_start: 0.3188 (OUTLIER) cc_final: 0.1562 (m-80)
REVERT: C  563 GLN cc_start: 0.8386 (mt0) cc_final: 0.7580 (mm110)
REVERT: H   80 TYR cc_start: 0.8547 (m-80) cc_final: 0.8320 (m-80)
  outliers start: 12
  outliers final: 10
  residues processed: 62
  average time/residue: 0.1676
  time to fit residues: 13.4900
Evaluate side-chains
  67 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain C residue  559 PHE
Chi-restraints excluded: chain C residue  581 THR
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain L residue   28 GLN
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   51 TYR
Chi-restraints excluded: chain L residue  105 LEU
Chi-restraints excluded: chain L residue  107 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.3515 r_free = 0.3515 target = 0.073108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.058012 restraints weight = 12802.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 3.81
r_work: 0.3029 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3917  Z= 0.257
  Angle     :  0.764  11.515   5322  Z= 0.375
  Chirality :  0.047   0.204    587
  Planarity :  0.004   0.035    679
  Dihedral  :  7.555  56.471    585
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.31 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.51 (0.40), residues: 477
  helix: -3.29 (0.70), residues: 33
  sheet:  1.12 (0.44), residues: 157
  loop : -0.83 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.004   0.001   HIS L  56 
 PHE   0.013   0.002   PHE C 392 
 TYR   0.035   0.002   TYR C 365 
 ARG   0.010   0.001   ARG L  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00101 (    1)
  link_NAG-ASN         : angle       9.19573 (    3)
  link_BETA1-4         : bond        0.00064 (    1)
  link_BETA1-4         : angle       1.27568 (    3)
  hydrogen bonds       : bond        0.03094 (  123)
  hydrogen bonds       : angle       5.57371 (  291)
  link_BETA1-6         : bond        0.02285 (    1)
  link_BETA1-6         : angle       1.57321 (    3)
  SS BOND              : bond        0.00666 (    6)
  SS BOND              : angle       2.02561 (   12)
  covalent geometry    : bond        0.00587 ( 3908)
  covalent geometry    : angle       0.72563 ( 5301)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2237.10 seconds
wall clock time: 39 minutes 46.89 seconds (2386.89 seconds total)