Starting phenix.real_space_refine
on Fri May  9 18:02:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8khd_37241/05_2025/8khd_37241.cif"
  }
  resolution = 3.5
  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=  -0.002 sd=   0.057
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      17      5.16       5
     C    2112      2.51       5
     N     561      2.21       5
     O     647      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: 3337
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 917
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "J"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 806
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1600
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 187}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.38, per 1000 atoms: 1.01
  Number of scatterers: 3337
  At special positions: 0
  Unit cell: (69.96, 90.1, 86.92, 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      17     16.00
     O     647      8.00
     N     561      7.00
     C    2112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  87 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.02
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 410.5 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 7 sheets defined
      3.5% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.696A  pdb=" N   ASP H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 405 through 408
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 50
      removed outlier: 6.501A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 104 through 106
      removed outlier: 4.357A  pdb=" N   VAL H 105 " --> pdb=" O   ARG C 466 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG C 466 " --> pdb=" O   VAL H 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'J' and resid 9 through 10
      removed outlier: 6.699A  pdb=" N   TRP J  34 " --> pdb=" O   VAL J  46 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 18 through 23
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.600A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASN C 437 " --> pdb=" O   PHE C 374 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   PHE C 374 " --> pdb=" O   ASN C 437 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454

    85 hydrogen bonds defined for protein.
    219 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: 0.81

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1087
        1.35 -     1.48: 932
        1.48 -     1.61: 1377
        1.61 -     1.74: 0
        1.74 -     1.87: 22
  Bond restraints: 3418
  Sorted by residual:
  bond pdb=" CG1 ILE C 434 "
       pdb=" CD1 ILE C 434 "
    ideal  model  delta    sigma   weight residual
    1.513  1.438  0.075 3.90e-02 6.57e+02 3.67e+00
  bond pdb=" CB  CYS C 432 "
       pdb=" SG  CYS C 432 "
    ideal  model  delta    sigma   weight residual
    1.808  1.865 -0.057 3.30e-02 9.18e+02 3.00e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.77e+00
  bond pdb=" CA  ASN C 331 "
       pdb=" C   ASN C 331 "
    ideal  model  delta    sigma   weight residual
    1.521  1.537 -0.016 9.90e-03 1.02e+04 2.67e+00
  bond pdb=" C   ASN C 331 "
       pdb=" N   ILE C 332 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.18e+00
  ... (remaining 3413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 4514
        2.33 -     4.66: 113
        4.66 -     6.99: 18
        6.99 -     9.32: 4
        9.32 -    11.65: 1
  Bond angle restraints: 4650
  Sorted by residual:
  angle pdb=" C   ASN C 331 "
        pdb=" N   ILE C 332 "
        pdb=" CA  ILE C 332 "
      ideal   model   delta    sigma   weight residual
     121.70  129.97   -8.27 1.80e+00 3.09e-01 2.11e+01
  angle pdb=" C   VAL J  97 "
        pdb=" N   ILE J  98 "
        pdb=" CA  ILE J  98 "
      ideal   model   delta    sigma   weight residual
     121.97  129.47   -7.50 1.80e+00 3.09e-01 1.73e+01
  angle pdb=" CB  MET H 122 "
        pdb=" CG  MET H 122 "
        pdb=" SD  MET H 122 "
      ideal   model   delta    sigma   weight residual
     112.70  124.35  -11.65 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" CA  CYS C 379 "
        pdb=" CB  CYS C 379 "
        pdb=" SG  CYS C 379 "
      ideal   model   delta    sigma   weight residual
     114.40  123.01   -8.61 2.30e+00 1.89e-01 1.40e+01
  angle pdb=" CA  TYR H 109 "
        pdb=" CB  TYR H 109 "
        pdb=" CG  TYR H 109 "
      ideal   model   delta    sigma   weight residual
     113.90  120.63   -6.73 1.80e+00 3.09e-01 1.40e+01
  ... (remaining 4645 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 1834
       17.62 -    35.25: 158
       35.25 -    52.87: 23
       52.87 -    70.49: 5
       70.49 -    88.11: 2
  Dihedral angle restraints: 2022
    sinusoidal: 781
      harmonic: 1241
  Sorted by residual:
  dihedral pdb=" CA  ALA C 372 "
           pdb=" C   ALA C 372 "
           pdb=" N   PRO C 373 "
           pdb=" CA  PRO C 373 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.61  -24.39     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  CYS C 379 "
           pdb=" C   CYS C 379 "
           pdb=" N   TYR C 380 "
           pdb=" CA  TYR C 380 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.93  -22.07     0      5.00e+00 4.00e-02 1.95e+01
  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   58.41   34.59     1      1.00e+01 1.00e-02 1.70e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 355
       0.045 -    0.089: 103
       0.089 -    0.134: 47
       0.134 -    0.178: 1
       0.178 -    0.223: 3
  Chirality restraints: 509
  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    2.66   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  THR H  59 "
            pdb=" CA  THR H  59 "
            pdb=" OG1 THR H  59 "
            pdb=" CG2 THR H  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  CYS C 379 "
            pdb=" N   CYS C 379 "
            pdb=" C   CYS C 379 "
            pdb=" CB  CYS C 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.87e-01
  ... (remaining 506 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 374 "    0.015 2.00e-02 2.50e+03   1.66e-02 4.82e+00
        pdb=" CG  PHE C 374 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 374 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 374 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 374 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 374 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 374 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET H 108 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.52e+00
        pdb=" C   MET H 108 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET H 108 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR H 109 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP J   7 "    0.033 5.00e-02 4.00e+02   5.07e-02 4.11e+00
        pdb=" N   PRO J   8 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO J   8 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO J   8 "    0.028 5.00e-02 4.00e+02
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 952
        2.81 -     3.33: 2787
        3.33 -     3.85: 5267
        3.85 -     4.38: 5755
        4.38 -     4.90: 10283
  Nonbonded interactions: 25044
  Sorted by model distance:
  nonbonded pdb=" OG  SER J  64 "
            pdb=" OG  SER J  71 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER J  66 "
            pdb=" OG1 THR J  69 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   VAL J  97 "
            pdb=" N   PHE J  99 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   ILE H  55 "
            pdb=" ND2 ASN C 354 "
     model   vdw
     2.355 3.120
  ... (remaining 25039 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:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.190
  Find NCS groups from input model:        0.030
  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:   18.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
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   0.075   3425  Z= 0.189
  Angle     :  0.884  11.654   4665  Z= 0.467
  Chirality :  0.050   0.223    509
  Planarity :  0.006   0.051    604
  Dihedral  : 13.417  88.113   1218
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.28 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.41), residues: 426
  helix: -4.55 (0.52), residues: 13
  sheet:  0.98 (0.49), residues: 122
  loop : -1.74 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 353 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.039   0.002   PHE C 374 
 TYR   0.034   0.002   TYR C 369 
 ARG   0.006   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00566 (    1)
  link_NAG-ASN         : angle       2.26007 (    3)
  hydrogen bonds       : bond        0.10069 (   85)
  hydrogen bonds       : angle       7.87130 (  219)
  SS BOND              : bond        0.01016 (    6)
  SS BOND              : angle       2.23600 (   12)
  covalent geometry    : bond        0.00405 ( 3418)
  covalent geometry    : angle       0.87647 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1825
  time to fit residues: 17.1083
Evaluate side-chains
  64 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
C 394 ASN
C 474 GLN
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.151079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.120595 restraints weight = 6115.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.125125 restraints weight = 3576.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.128207 restraints weight = 2561.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3425  Z= 0.142
  Angle     :  0.630   7.937   4665  Z= 0.329
  Chirality :  0.043   0.174    509
  Planarity :  0.005   0.043    604
  Dihedral  :  5.568  29.497    496
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.51 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 10.64 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -1.26 (0.41), residues: 426
  helix: -4.32 (0.67), residues: 19
  sheet:  1.23 (0.49), residues: 121
  loop : -1.65 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.010   0.001   PHE C 400 
 TYR   0.012   0.001   TYR J  48 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00357 (    1)
  link_NAG-ASN         : angle       2.21960 (    3)
  hydrogen bonds       : bond        0.03394 (   85)
  hydrogen bonds       : angle       5.97015 (  219)
  SS BOND              : bond        0.00608 (    6)
  SS BOND              : angle       1.63648 (   12)
  covalent geometry    : bond        0.00325 ( 3418)
  covalent geometry    : angle       0.62306 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  107 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6388 (ptp)
REVERT: J   48 TYR cc_start: 0.7326 (p90) cc_final: 0.7104 (p90)
REVERT: J   69 THR cc_start: 0.8504 (p) cc_final: 0.8172 (p)
  outliers start: 10
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1483
  time to fit residues: 13.6152
Evaluate side-chains
  66 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  107 MET
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0270
   overall best weight:    0.9240

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.155757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.123404 restraints weight = 6283.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.128173 restraints weight = 3479.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.131306 restraints weight = 2459.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3425  Z= 0.128
  Angle     :  0.610   8.073   4665  Z= 0.313
  Chirality :  0.043   0.169    509
  Planarity :  0.004   0.040    604
  Dihedral  :  5.213  26.874    496
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.75 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.81 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -0.99 (0.41), residues: 426
  helix: -3.56 (1.21), residues: 12
  sheet:  1.33 (0.48), residues: 119
  loop : -1.51 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.008   0.001   PHE C 400 
 TYR   0.013   0.001   TYR C 380 
 ARG   0.002   0.000   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       2.03156 (    3)
  hydrogen bonds       : bond        0.03144 (   85)
  hydrogen bonds       : angle       5.58588 (  219)
  SS BOND              : bond        0.00809 (    6)
  SS BOND              : angle       1.48910 (   12)
  covalent geometry    : bond        0.00292 ( 3418)
  covalent geometry    : angle       0.60439 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   92 ASP cc_start: 0.7934 (m-30) cc_final: 0.7733 (m-30)
REVERT: J   48 TYR cc_start: 0.7391 (p90) cc_final: 0.6792 (p90)
REVERT: J   69 THR cc_start: 0.8489 (p) cc_final: 0.8166 (p)
REVERT: C  390 LEU cc_start: 0.7367 (pt) cc_final: 0.6896 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1717
  time to fit residues: 15.9168
Evaluate side-chains
  70 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   overall best weight:    1.1764

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

Flipped N/Q/H residues before XYZ refinement:
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.152645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.120974 restraints weight = 6401.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125462 restraints weight = 3602.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.128522 restraints weight = 2552.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3425  Z= 0.146
  Angle     :  0.622   7.886   4665  Z= 0.320
  Chirality :  0.044   0.171    509
  Planarity :  0.004   0.039    604
  Dihedral  :  5.245  26.445    496
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.98 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.05 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: 426
  helix: -3.57 (1.24), residues: 13
  sheet:  1.26 (0.49), residues: 119
  loop : -1.48 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.015   0.001   PHE C 338 
 TYR   0.010   0.001   TYR C 380 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00424 (    1)
  link_NAG-ASN         : angle       2.33389 (    3)
  hydrogen bonds       : bond        0.03276 (   85)
  hydrogen bonds       : angle       5.42981 (  219)
  SS BOND              : bond        0.00591 (    6)
  SS BOND              : angle       1.54108 (   12)
  covalent geometry    : bond        0.00340 ( 3418)
  covalent geometry    : angle       0.61569 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   48 TYR cc_start: 0.7535 (p90) cc_final: 0.7299 (p90)
REVERT: J   69 THR cc_start: 0.8480 (p) cc_final: 0.8145 (p)
REVERT: C  357 ARG cc_start: 0.7757 (tpt-90) cc_final: 0.7539 (tpt-90)
REVERT: C  360 ASN cc_start: 0.8830 (m110) cc_final: 0.8540 (m110)
  outliers start: 8
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1388
  time to fit residues: 13.1784
Evaluate side-chains
  71 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0770
   chunk 22 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    0.7138

-------------------------------------------------------------------------------
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 = 0.4214 r_free = 0.4214 target = 0.150043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.126619 restraints weight = 6192.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.129771 restraints weight = 3838.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.132227 restraints weight = 2931.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3425  Z= 0.116
  Angle     :  0.615   8.334   4665  Z= 0.315
  Chirality :  0.043   0.165    509
  Planarity :  0.004   0.037    604
  Dihedral  :  5.099  24.701    496
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.98 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 18.21 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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 (0.42), residues: 426
  helix: -3.97 (0.72), residues: 19
  sheet:  1.10 (0.48), residues: 125
  loop : -1.50 (0.38), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.008   0.001   PHE C 338 
 TYR   0.011   0.001   TYR H  97 
 ARG   0.002   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00457 (    1)
  link_NAG-ASN         : angle       2.22890 (    3)
  hydrogen bonds       : bond        0.02928 (   85)
  hydrogen bonds       : angle       5.26562 (  219)
  SS BOND              : bond        0.00561 (    6)
  SS BOND              : angle       1.62738 (   12)
  covalent geometry    : bond        0.00262 ( 3418)
  covalent geometry    : angle       0.60728 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   92 ASP cc_start: 0.7931 (m-30) cc_final: 0.7717 (m-30)
REVERT: J   48 TYR cc_start: 0.7397 (p90) cc_final: 0.6934 (p90)
REVERT: J   69 THR cc_start: 0.8510 (p) cc_final: 0.8194 (p)
REVERT: C  360 ASN cc_start: 0.8803 (m110) cc_final: 0.8490 (m110)
REVERT: C  390 LEU cc_start: 0.7386 (pt) cc_final: 0.6889 (tt)
REVERT: C  406 GLU cc_start: 0.7214 (pm20) cc_final: 0.6957 (mp0)
  outliers start: 9
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1418
  time to fit residues: 14.0276
Evaluate side-chains
  71 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 8 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0980
   chunk 13 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.149957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.120718 restraints weight = 6337.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125307 restraints weight = 3493.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.128319 restraints weight = 2462.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3425  Z= 0.126
  Angle     :  0.617   7.575   4665  Z= 0.315
  Chirality :  0.044   0.164    509
  Planarity :  0.004   0.037    604
  Dihedral  :  5.049  24.565    496
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.22 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.21 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -1.03 (0.42), residues: 426
  helix: -4.02 (0.65), residues: 19
  sheet:  1.28 (0.49), residues: 120
  loop : -1.42 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.007   0.001   PHE C 400 
 TYR   0.011   0.001   TYR C 380 
 ARG   0.002   0.000   ARG J  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00431 (    1)
  link_NAG-ASN         : angle       2.30070 (    3)
  hydrogen bonds       : bond        0.02971 (   85)
  hydrogen bonds       : angle       5.25636 (  219)
  SS BOND              : bond        0.00711 (    6)
  SS BOND              : angle       1.89211 (   12)
  covalent geometry    : bond        0.00293 ( 3418)
  covalent geometry    : angle       0.60723 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  119 GLN cc_start: 0.7509 (pp30) cc_final: 0.7269 (pp30)
REVERT: J   48 TYR cc_start: 0.7498 (p90) cc_final: 0.6975 (p90)
REVERT: J   69 THR cc_start: 0.8493 (p) cc_final: 0.8188 (p)
REVERT: C  360 ASN cc_start: 0.8725 (m110) cc_final: 0.8449 (m110)
REVERT: C  390 LEU cc_start: 0.7521 (pt) cc_final: 0.7075 (tt)
REVERT: C  406 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6884 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1369
  time to fit residues: 13.5021
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  406 GLU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0470
   chunk 23 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.149881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.126710 restraints weight = 6169.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.129625 restraints weight = 3956.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.132585 restraints weight = 3002.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3425  Z= 0.110
  Angle     :  0.601   7.002   4665  Z= 0.306
  Chirality :  0.043   0.161    509
  Planarity :  0.004   0.037    604
  Dihedral  :  4.907  23.317    496
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.75 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.21 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -0.99 (0.43), residues: 426
  helix: -3.82 (0.72), residues: 19
  sheet:  1.08 (0.48), residues: 125
  loop : -1.34 (0.39), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.009   0.001   PHE C 374 
 TYR   0.012   0.001   TYR C 380 
 ARG   0.002   0.000   ARG J  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00468 (    1)
  link_NAG-ASN         : angle       2.22325 (    3)
  hydrogen bonds       : bond        0.02777 (   85)
  hydrogen bonds       : angle       5.10978 (  219)
  SS BOND              : bond        0.00592 (    6)
  SS BOND              : angle       1.56619 (   12)
  covalent geometry    : bond        0.00252 ( 3418)
  covalent geometry    : angle       0.59351 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   48 TYR cc_start: 0.7389 (p90) cc_final: 0.6934 (p90)
REVERT: J   69 THR cc_start: 0.8456 (p) cc_final: 0.8149 (p)
REVERT: J  104 LYS cc_start: 0.6979 (ttmm) cc_final: 0.6138 (tmtt)
REVERT: C  360 ASN cc_start: 0.8819 (m110) cc_final: 0.8539 (m110)
REVERT: C  390 LEU cc_start: 0.7449 (pt) cc_final: 0.6977 (tt)
REVERT: C  406 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6934 (mp0)
  outliers start: 11
  outliers final: 8
  residues processed: 82
  average time/residue: 0.1434
  time to fit residues: 14.5833
Evaluate side-chains
  77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue    7 ASP
Chi-restraints excluded: chain J residue   47 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  406 GLU
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0870
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 37 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0050
   chunk 14 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.2372

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

Flipped N/Q/H residues before XYZ refinement:
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.151442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.122390 restraints weight = 6269.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.127118 restraints weight = 3409.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.130374 restraints weight = 2373.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3425  Z= 0.108
  Angle     :  0.639   9.254   4665  Z= 0.322
  Chirality :  0.043   0.157    509
  Planarity :  0.004   0.037    604
  Dihedral  :  4.794  20.915    496
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.04 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.13 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -0.96 (0.43), residues: 426
  helix: -3.66 (0.79), residues: 19
  sheet:  0.92 (0.47), residues: 132
  loop : -1.28 (0.40), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.009   0.001   PHE H  82 
 TYR   0.012   0.001   TYR C 380 
 ARG   0.006   0.001   ARG C 357 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00450 (    1)
  link_NAG-ASN         : angle       2.09905 (    3)
  hydrogen bonds       : bond        0.02640 (   85)
  hydrogen bonds       : angle       5.04938 (  219)
  SS BOND              : bond        0.00506 (    6)
  SS BOND              : angle       1.60111 (   12)
  covalent geometry    : bond        0.00238 ( 3418)
  covalent geometry    : angle       0.63258 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: J   48 TYR cc_start: 0.7199 (p90) cc_final: 0.6530 (p90)
REVERT: J   69 THR cc_start: 0.8508 (p) cc_final: 0.8267 (p)
REVERT: J  104 LYS cc_start: 0.6947 (ttmm) cc_final: 0.6100 (tmtt)
REVERT: C  360 ASN cc_start: 0.8800 (m110) cc_final: 0.8520 (m110)
REVERT: C  390 LEU cc_start: 0.7428 (pt) cc_final: 0.6977 (tt)
REVERT: C  406 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6816 (mp0)
REVERT: C  474 GLN cc_start: 0.3849 (tp40) cc_final: 0.3640 (tp40)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1445
  time to fit residues: 13.5440
Evaluate side-chains
  73 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  406 GLU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.0070
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 16 optimal weight:    0.2980
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.2602

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

Flipped N/Q/H residues before XYZ refinement:
J  36 GLN
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.147830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.117823 restraints weight = 6273.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.122441 restraints weight = 3494.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.125532 restraints weight = 2485.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3425  Z= 0.161
  Angle     :  0.680   9.002   4665  Z= 0.350
  Chirality :  0.044   0.162    509
  Planarity :  0.005   0.045    604
  Dihedral  :  5.107  22.560    496
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.45 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.29 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -0.98 (0.42), residues: 426
  helix: -3.55 (0.85), residues: 19
  sheet:  1.09 (0.47), residues: 122
  loop : -1.32 (0.39), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.009   0.001   PHE H  82 
 TYR   0.014   0.001   TYR J  31 
 ARG   0.003   0.001   ARG J  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00424 (    1)
  link_NAG-ASN         : angle       2.28026 (    3)
  hydrogen bonds       : bond        0.03143 (   85)
  hydrogen bonds       : angle       5.20793 (  219)
  SS BOND              : bond        0.00676 (    6)
  SS BOND              : angle       1.76987 (   12)
  covalent geometry    : bond        0.00370 ( 3418)
  covalent geometry    : angle       0.67255 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: J   48 TYR cc_start: 0.7513 (p90) cc_final: 0.7018 (p90)
REVERT: J   69 THR cc_start: 0.8544 (p) cc_final: 0.8288 (p)
REVERT: J  104 LYS cc_start: 0.7104 (ttmm) cc_final: 0.6258 (tmtt)
REVERT: C  360 ASN cc_start: 0.8855 (m110) cc_final: 0.8577 (m110)
REVERT: C  406 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6779 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1519
  time to fit residues: 14.3159
Evaluate side-chains
  78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue   47 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  406 GLU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  488 CYS
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 1 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
J  36 GLN
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 360 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.154231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.120931 restraints weight = 6629.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.125891 restraints weight = 3657.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.129068 restraints weight = 2595.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3425  Z= 0.153
  Angle     :  0.719  10.941   4665  Z= 0.366
  Chirality :  0.044   0.162    509
  Planarity :  0.005   0.059    604
  Dihedral  :  5.153  21.653    496
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  9.15 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 22.69 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -1.09 (0.42), residues: 426
  helix: -3.58 (0.87), residues: 19
  sheet:  0.77 (0.45), residues: 130
  loop : -1.34 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 436 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.010   0.001   PHE H  82 
 TYR   0.013   0.001   TYR H  97 
 ARG   0.003   0.000   ARG J  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00450 (    1)
  link_NAG-ASN         : angle       2.26508 (    3)
  hydrogen bonds       : bond        0.03156 (   85)
  hydrogen bonds       : angle       5.29961 (  219)
  SS BOND              : bond        0.00646 (    6)
  SS BOND              : angle       1.74027 (   12)
  covalent geometry    : bond        0.00354 ( 3418)
  covalent geometry    : angle       0.71202 ( 4650)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: H   92 ASP cc_start: 0.8188 (m-30) cc_final: 0.7981 (m-30)
REVERT: J   48 TYR cc_start: 0.7592 (p90) cc_final: 0.6897 (p90)
REVERT: J   69 THR cc_start: 0.8626 (p) cc_final: 0.8398 (p)
REVERT: J  104 LYS cc_start: 0.7017 (ttmm) cc_final: 0.6120 (tmtt)
REVERT: C  360 ASN cc_start: 0.8817 (m-40) cc_final: 0.8584 (m110)
REVERT: C  406 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6794 (mp0)
  outliers start: 10
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1518
  time to fit residues: 13.4025
Evaluate side-chains
  76 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain J residue   47 ILE
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  402 ILE
Chi-restraints excluded: chain C residue  406 GLU
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  488 CYS
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain C residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0060
   chunk 21 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
** J  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.155016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.123120 restraints weight = 6713.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.128047 restraints weight = 3614.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.131166 restraints weight = 2537.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3425  Z= 0.138
  Angle     :  0.713  12.308   4665  Z= 0.361
  Chirality :  0.044   0.162    509
  Planarity :  0.005   0.045    604
  Dihedral  :  4.987  19.789    496
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.92 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 23.81 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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: -1.05 (0.42), residues: 426
  helix: -3.41 (0.93), residues: 18
  sheet:  0.72 (0.45), residues: 131
  loop : -1.29 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  36 
 HIS   0.002   0.001   HIS J  96 
 PHE   0.009   0.001   PHE H  82 
 TYR   0.014   0.001   TYR H  97 
 ARG   0.002   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00443 (    1)
  link_NAG-ASN         : angle       2.23705 (    3)
  hydrogen bonds       : bond        0.02966 (   85)
  hydrogen bonds       : angle       5.26586 (  219)
  SS BOND              : bond        0.00627 (    6)
  SS BOND              : angle       1.64315 (   12)
  covalent geometry    : bond        0.00317 ( 3418)
  covalent geometry    : angle       0.70686 ( 4650)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1634.07 seconds
wall clock time: 29 minutes 14.78 seconds (1754.78 seconds total)