Starting phenix.real_space_refine
on Thu Jul 24 17:36:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2025/8b7q_15899.cif"
  }
  resolution = 4.02
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic.
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    2236      2.51       5
     N     594      2.21       5
     O     663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3511
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1064
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1637
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      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: 3.95, per 1000 atoms: 1.13
  Number of scatterers: 3511
  At special positions: 0
  Unit cell: (79.584, 98.651, 88.703, 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     663      8.00
     N     594      7.00
     C    2236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " 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 F 901 " - " ASN F 345 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 410.9 milliseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      25.9% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.870A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 4.117A  pdb=" N   ASP A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.963A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.536A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546
      removed outlier: 5.035A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334
      removed outlier: 3.552A  pdb=" N   ALA F 346 " --> pdb=" O   PHE F 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340
      removed outlier: 7.582A  pdb=" N   HIS F 417 " --> pdb=" O   ASN F 412 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ASN F 412 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG F 419 " --> pdb=" O   CYS F 410 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   CYS F 410 " --> pdb=" O   ARG F 419 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    474 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: 0.95

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1124
        1.34 -     1.46: 812
        1.46 -     1.58: 1630
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" C1  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C5  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG F 901 "
       pdb=" O3  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.76e-01
  bond pdb=" C   TRP B 447 "
       pdb=" N   SER B 448 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.92e-02 2.71e+03 6.28e-01
  bond pdb=" N   SER A 114 "
       pdb=" CA  SER A 114 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.008 1.08e-02 8.57e+03 5.33e-01
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4692
        1.40 -     2.81: 165
        2.81 -     4.21: 26
        4.21 -     5.62: 1
        5.62 -     7.02: 1
  Bond angle restraints: 4885
  Sorted by residual:
  angle pdb=" C   ILE A  63 "
        pdb=" N   PRO A  64 "
        pdb=" CA  PRO A  64 "
      ideal   model   delta    sigma   weight residual
     119.84  122.92   -3.08 1.25e+00 6.40e-01 6.05e+00
  angle pdb=" C   PHE A 113 "
        pdb=" N   SER A 114 "
        pdb=" CA  SER A 114 "
      ideal   model   delta    sigma   weight residual
     120.89  124.35   -3.46 1.50e+00 4.44e-01 5.32e+00
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.65e+00 3.67e-01 5.30e+00
  angle pdb=" C   ILE A  45 "
        pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
      ideal   model   delta    sigma   weight residual
     120.82  124.00   -3.18 1.50e+00 4.44e-01 4.50e+00
  angle pdb=" N   LEU B 503 "
        pdb=" CA  LEU B 503 "
        pdb=" C   LEU B 503 "
      ideal   model   delta    sigma   weight residual
     111.33  113.75   -2.42 1.21e+00 6.83e-01 4.01e+00
  ... (remaining 4880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 2086
       15.92 -    31.83: 94
       31.83 -    47.75: 22
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2208
    sinusoidal: 903
      harmonic: 1305
  Sorted by residual:
  dihedral pdb=" CB  CYS F 350 "
           pdb=" SG  CYS F 350 "
           pdb=" SG  CYS F 410 "
           pdb=" CB  CYS F 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.39   29.61     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" N   LEU A 161 "
           pdb=" CA  LEU A 161 "
           pdb=" CB  LEU A 161 "
           pdb=" CG  LEU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.82  -58.18     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   PHE F 334 "
           pdb=" CA  PHE F 334 "
           pdb=" CB  PHE F 334 "
           pdb=" CG  PHE F 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.09   51.09     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 2205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 349
       0.031 -    0.062: 154
       0.062 -    0.092: 33
       0.092 -    0.123: 31
       0.123 -    0.154: 5
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" CA  ILE F 351 "
            pdb=" N   ILE F 351 "
            pdb=" C   ILE F 351 "
            pdb=" CB  ILE F 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  PRO A  64 "
            pdb=" N   PRO A  64 "
            pdb=" C   PRO A  64 "
            pdb=" CB  PRO A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE F 374 "
            pdb=" N   ILE F 374 "
            pdb=" C   ILE F 374 "
            pdb=" CB  ILE F 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLN A 155 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 448 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO B 449 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 148 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 148 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 148 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 149 "    0.007 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 532
        2.77 -     3.30: 3250
        3.30 -     3.83: 5553
        3.83 -     4.37: 6419
        4.37 -     4.90: 11088
  Nonbonded interactions: 26842
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 141 "
            pdb=" OH  TYR F 409 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   PRO A  64 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD2 ASP A  30 "
            pdb=" OH  TYR B 470 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG B 571 "
            pdb=" OE1 GLN B 608 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH2 ARG F 400 "
            pdb=" O   TYR F 405 "
     model   vdw
     2.378 3.120
  ... (remaining 26837 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:             5.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.180
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3595  Z= 0.121
  Angle     :  0.601   7.021   4900  Z= 0.335
  Chirality :  0.043   0.154    572
  Planarity :  0.004   0.035    615
  Dihedral  :  9.873  79.577   1340
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.93 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.13 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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:  0.29 (0.38), residues: 433
  helix:  0.92 (0.47), residues: 97
  sheet:  0.83 (0.39), residues: 134
  loop : -0.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.010   0.001   PHE B 493 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.002   0.000   ARG B 467 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.67786 (    3)
  hydrogen bonds       : bond        0.18058 (  159)
  hydrogen bonds       : angle       7.45858 (  474)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.89249 (   12)
  covalent geometry    : bond        0.00265 ( 3588)
  covalent geometry    : angle       0.59895 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm)
REVERT: A   63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt)
REVERT: A   93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40)
REVERT: B  436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m)
REVERT: B  540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0)
REVERT: B  565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0)
REVERT: B  572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90)
REVERT: B  585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20)
REVERT: B  609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m)
REVERT: B  612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90)
REVERT: F  365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p)
REVERT: F  388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp)
REVERT: F  393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0)
  outliers start: 12
  outliers final: 2
  residues processed: 155
  average time/residue: 0.1634
  time to fit residues: 30.4227
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.112267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.091989 restraints weight = 8036.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.094721 restraints weight = 4715.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.096557 restraints weight = 3257.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3595  Z= 0.164
  Angle     :  0.671  11.033   4900  Z= 0.341
  Chirality :  0.046   0.261    572
  Planarity :  0.004   0.043    615
  Dihedral  :  4.389  17.576    496
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  1.72 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.40), residues: 433
  helix:  2.28 (0.50), residues: 103
  sheet:  0.53 (0.40), residues: 127
  loop :  0.11 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 620 
 HIS   0.005   0.001   HIS F 418 
 PHE   0.013   0.002   PHE F 348 
 TYR   0.020   0.002   TYR A  82 
 ARG   0.004   0.000   ARG F 419 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    1)
  link_NAG-ASN         : angle       2.00761 (    3)
  hydrogen bonds       : bond        0.04163 (  159)
  hydrogen bonds       : angle       5.19963 (  474)
  SS BOND              : bond        0.00494 (    6)
  SS BOND              : angle       3.74568 (   12)
  covalent geometry    : bond        0.00375 ( 3588)
  covalent geometry    : angle       0.64368 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8147 (ttpt)
REVERT: A   93 ASN cc_start: 0.7716 (m-40) cc_final: 0.7487 (m-40)
REVERT: B  429 ASN cc_start: 0.8859 (t0) cc_final: 0.8559 (t0)
REVERT: B  572 TYR cc_start: 0.8144 (p90) cc_final: 0.7745 (p90)
REVERT: B  609 VAL cc_start: 0.9508 (t) cc_final: 0.9302 (m)
REVERT: B  612 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8322 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8683 (pt) cc_final: 0.8472 (mm)
REVERT: F  393 ASN cc_start: 0.7562 (t0) cc_final: 0.7057 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1441
  time to fit residues: 20.1443
Evaluate side-chains
  92 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
B 499 GLN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.111633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.090729 restraints weight = 8061.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093365 restraints weight = 4864.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095187 restraints weight = 3416.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3595  Z= 0.163
  Angle     :  0.648  14.331   4900  Z= 0.333
  Chirality :  0.047   0.232    572
  Planarity :  0.004   0.035    615
  Dihedral  :  4.437  25.983    496
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.96 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.41), residues: 433
  helix:  2.63 (0.50), residues: 102
  sheet:  0.60 (0.40), residues: 129
  loop :  0.36 (0.47), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 348 
 TYR   0.017   0.002   TYR F 352 
 ARG   0.005   0.000   ARG F 368 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00177 (    1)
  link_NAG-ASN         : angle       2.22214 (    3)
  hydrogen bonds       : bond        0.04012 (  159)
  hydrogen bonds       : angle       4.87796 (  474)
  SS BOND              : bond        0.00818 (    6)
  SS BOND              : angle       3.26138 (   12)
  covalent geometry    : bond        0.00376 ( 3588)
  covalent geometry    : angle       0.62630 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8329 (ttpt)
REVERT: B  429 ASN cc_start: 0.8916 (t0) cc_final: 0.8620 (t0)
REVERT: B  437 ASP cc_start: 0.8930 (p0) cc_final: 0.8715 (p0)
REVERT: B  609 VAL cc_start: 0.9459 (t) cc_final: 0.9216 (m)
REVERT: B  612 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8472 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8674 (pt) cc_final: 0.8364 (mm)
REVERT: F  393 ASN cc_start: 0.7683 (t0) cc_final: 0.6954 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1609
  time to fit residues: 20.6563
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.111554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.091032 restraints weight = 8042.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.093659 restraints weight = 4921.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.095511 restraints weight = 3484.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.4430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3595  Z= 0.141
  Angle     :  0.623  12.038   4900  Z= 0.316
  Chirality :  0.045   0.201    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.464  24.472    496
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.21 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.41), residues: 433
  helix:  2.71 (0.50), residues: 102
  sheet:  0.76 (0.42), residues: 128
  loop :  0.19 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.009   0.001   PHE F 348 
 TYR   0.019   0.002   TYR B 572 
 ARG   0.003   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00111 (    1)
  link_NAG-ASN         : angle       2.24424 (    3)
  hydrogen bonds       : bond        0.03846 (  159)
  hydrogen bonds       : angle       4.64920 (  474)
  SS BOND              : bond        0.00571 (    6)
  SS BOND              : angle       3.19255 (   12)
  covalent geometry    : bond        0.00329 ( 3588)
  covalent geometry    : angle       0.60067 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8213 (ptm160)
REVERT: A   69 ILE cc_start: 0.7223 (tp) cc_final: 0.6935 (tp)
REVERT: A   74 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8223 (ttpt)
REVERT: B  429 ASN cc_start: 0.8929 (t0) cc_final: 0.8625 (t0)
REVERT: B  542 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8285 (mmtm)
REVERT: B  609 VAL cc_start: 0.9439 (t) cc_final: 0.9175 (m)
REVERT: B  612 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8377 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8668 (pt) cc_final: 0.8304 (mm)
REVERT: F  393 ASN cc_start: 0.7547 (t0) cc_final: 0.6499 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1457
  time to fit residues: 18.5649
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.109896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.088950 restraints weight = 8347.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.091561 restraints weight = 4991.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.093414 restraints weight = 3519.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3595  Z= 0.161
  Angle     :  0.646  12.075   4900  Z= 0.329
  Chirality :  0.046   0.196    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.662  32.279    496
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.41 (0.41), residues: 433
  helix:  3.19 (0.51), residues: 96
  sheet:  0.75 (0.42), residues: 128
  loop :  0.02 (0.46), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 
 PHE   0.011   0.001   PHE F 334 
 TYR   0.012   0.001   TYR F 424 
 ARG   0.004   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00201 (    1)
  link_NAG-ASN         : angle       2.46281 (    3)
  hydrogen bonds       : bond        0.03872 (  159)
  hydrogen bonds       : angle       4.63617 (  474)
  SS BOND              : bond        0.00712 (    6)
  SS BOND              : angle       3.63085 (   12)
  covalent geometry    : bond        0.00371 ( 3588)
  covalent geometry    : angle       0.61850 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8209 (ptm160)
REVERT: A   69 ILE cc_start: 0.7156 (tp) cc_final: 0.6946 (tp)
REVERT: A   74 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8295 (ttpt)
REVERT: B  429 ASN cc_start: 0.8906 (t0) cc_final: 0.8626 (t0)
REVERT: B  437 ASP cc_start: 0.8812 (p0) cc_final: 0.8601 (p0)
REVERT: B  453 GLN cc_start: 0.8782 (pt0) cc_final: 0.8280 (pm20)
REVERT: B  542 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8283 (mmtm)
REVERT: B  572 TYR cc_start: 0.8017 (p90) cc_final: 0.7656 (p90)
REVERT: B  612 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8497 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7588 (t0) cc_final: 0.6474 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1469
  time to fit residues: 17.9795
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.108811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.088195 restraints weight = 8444.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.090794 restraints weight = 5223.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.092608 restraints weight = 3705.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.4911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3595  Z= 0.173
  Angle     :  0.656  10.494   4900  Z= 0.334
  Chirality :  0.046   0.195    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.773  32.547    496
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.20 (0.41), residues: 433
  helix:  2.62 (0.52), residues: 102
  sheet:  0.75 (0.42), residues: 128
  loop : -0.07 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 366 
 HIS   0.005   0.001   HIS B 465 
 PHE   0.014   0.001   PHE F 334 
 TYR   0.018   0.002   TYR A  82 
 ARG   0.006   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00250 (    1)
  link_NAG-ASN         : angle       2.64909 (    3)
  hydrogen bonds       : bond        0.03996 (  159)
  hydrogen bonds       : angle       4.77813 (  474)
  SS BOND              : bond        0.00493 (    6)
  SS BOND              : angle       3.72222 (   12)
  covalent geometry    : bond        0.00398 ( 3588)
  covalent geometry    : angle       0.62718 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8213 (ptm160)
REVERT: A   69 ILE cc_start: 0.7185 (tp) cc_final: 0.6842 (tp)
REVERT: A   74 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8322 (ttpt)
REVERT: B  429 ASN cc_start: 0.8879 (t0) cc_final: 0.8605 (t0)
REVERT: B  437 ASP cc_start: 0.8843 (p0) cc_final: 0.8613 (p0)
REVERT: B  453 GLN cc_start: 0.8759 (pt0) cc_final: 0.8187 (pm20)
REVERT: B  542 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8309 (mmtm)
REVERT: B  572 TYR cc_start: 0.8031 (p90) cc_final: 0.7648 (p90)
REVERT: B  612 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8556 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7564 (t0) cc_final: 0.6692 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1460
  time to fit residues: 18.1646
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.111124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.090926 restraints weight = 8050.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.093533 restraints weight = 4930.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.095356 restraints weight = 3463.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.5176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3595  Z= 0.127
  Angle     :  0.612   9.699   4900  Z= 0.313
  Chirality :  0.045   0.176    572
  Planarity :  0.004   0.028    615
  Dihedral  :  4.515  30.292    496
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.41), residues: 433
  helix:  2.34 (0.51), residues: 108
  sheet:  0.89 (0.43), residues: 127
  loop : -0.16 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.008   0.001   PHE F 334 
 TYR   0.009   0.001   TYR F 424 
 ARG   0.002   0.000   ARG A  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00074 (    1)
  link_NAG-ASN         : angle       2.23948 (    3)
  hydrogen bonds       : bond        0.03690 (  159)
  hydrogen bonds       : angle       4.56231 (  474)
  SS BOND              : bond        0.00422 (    6)
  SS BOND              : angle       3.17876 (   12)
  covalent geometry    : bond        0.00292 ( 3588)
  covalent geometry    : angle       0.59024 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8204 (ptm160)
REVERT: A   69 ILE cc_start: 0.7096 (tp) cc_final: 0.6542 (tp)
REVERT: A   74 LYS cc_start: 0.8536 (ttpt) cc_final: 0.8229 (ttpt)
REVERT: B  429 ASN cc_start: 0.8855 (t0) cc_final: 0.8588 (t0)
REVERT: B  453 GLN cc_start: 0.8669 (pt0) cc_final: 0.8127 (pm20)
REVERT: B  542 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8324 (mmtm)
REVERT: B  612 ARG cc_start: 0.8912 (ttt180) cc_final: 0.8590 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7600 (t0) cc_final: 0.6734 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1524
  time to fit residues: 19.2536
Evaluate side-chains
  83 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0980
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.110471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.090684 restraints weight = 8299.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.093136 restraints weight = 5112.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.094847 restraints weight = 3644.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.5281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3595  Z= 0.136
  Angle     :  0.635   9.319   4900  Z= 0.321
  Chirality :  0.045   0.176    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.607  34.143    496
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.41), residues: 433
  helix:  2.33 (0.51), residues: 108
  sheet:  0.76 (0.43), residues: 128
  loop : -0.18 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.013   0.001   PHE F 348 
 TYR   0.010   0.001   TYR F 424 
 ARG   0.001   0.000   ARG F 385 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00114 (    1)
  link_NAG-ASN         : angle       2.22570 (    3)
  hydrogen bonds       : bond        0.03747 (  159)
  hydrogen bonds       : angle       4.60343 (  474)
  SS BOND              : bond        0.00375 (    6)
  SS BOND              : angle       3.60761 (   12)
  covalent geometry    : bond        0.00314 ( 3588)
  covalent geometry    : angle       0.60741 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8184 (ptm160)
REVERT: A   69 ILE cc_start: 0.7038 (tp) cc_final: 0.6624 (tp)
REVERT: A   74 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8287 (ttpt)
REVERT: B  429 ASN cc_start: 0.8829 (t0) cc_final: 0.8584 (t0)
REVERT: B  542 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8356 (mmtm)
REVERT: B  572 TYR cc_start: 0.8059 (p90) cc_final: 0.7667 (p90)
REVERT: B  612 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8603 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7492 (t0) cc_final: 0.6666 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1474
  time to fit residues: 18.1943
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.109807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.090055 restraints weight = 8126.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.092478 restraints weight = 5081.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.094211 restraints weight = 3639.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3595  Z= 0.166
  Angle     :  0.652  10.022   4900  Z= 0.334
  Chirality :  0.046   0.177    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.819  37.890    496
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.07 (0.41), residues: 433
  helix:  2.51 (0.51), residues: 102
  sheet:  0.65 (0.44), residues: 130
  loop : -0.15 (0.45), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 447 
 HIS   0.005   0.001   HIS B 465 
 PHE   0.013   0.001   PHE F 348 
 TYR   0.013   0.002   TYR A  82 
 ARG   0.002   0.000   ARG F 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00220 (    1)
  link_NAG-ASN         : angle       2.51704 (    3)
  hydrogen bonds       : bond        0.03901 (  159)
  hydrogen bonds       : angle       4.75982 (  474)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       3.77622 (   12)
  covalent geometry    : bond        0.00386 ( 3588)
  covalent geometry    : angle       0.62234 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8201 (ptm160)
REVERT: A   69 ILE cc_start: 0.7013 (tp) cc_final: 0.6529 (tp)
REVERT: A   74 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8239 (ttpt)
REVERT: B  429 ASN cc_start: 0.8831 (t0) cc_final: 0.8578 (t0)
REVERT: B  453 GLN cc_start: 0.8750 (pt0) cc_final: 0.8257 (pm20)
REVERT: B  612 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8631 (ttt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1436
  time to fit residues: 17.3982
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:    0.0370
   chunk 9 optimal weight:    0.0370
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0970
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0040
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.1746

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
F 369 ASN
** F 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.113991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.094316 restraints weight = 8104.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.096841 restraints weight = 4950.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.098619 restraints weight = 3486.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3595  Z= 0.104
  Angle     :  0.602   8.459   4900  Z= 0.307
  Chirality :  0.044   0.179    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.490  36.838    496
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.41), residues: 433
  helix:  2.49 (0.51), residues: 108
  sheet:  0.79 (0.43), residues: 129
  loop : -0.07 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 623 
 HIS   0.001   0.000   HIS B 465 
 PHE   0.013   0.001   PHE F 348 
 TYR   0.006   0.001   TYR B 494 
 ARG   0.002   0.000   ARG F 385 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00089 (    1)
  link_NAG-ASN         : angle       1.62215 (    3)
  hydrogen bonds       : bond        0.03462 (  159)
  hydrogen bonds       : angle       4.48638 (  474)
  SS BOND              : bond        0.00378 (    6)
  SS BOND              : angle       3.36498 (   12)
  covalent geometry    : bond        0.00236 ( 3588)
  covalent geometry    : angle       0.57798 ( 4885)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8214 (ptm160)
REVERT: B  429 ASN cc_start: 0.8782 (t0) cc_final: 0.8557 (t0)
REVERT: B  612 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8646 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7534 (t0) cc_final: 0.6699 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1659
  time to fit residues: 21.1090
Evaluate side-chains
  84 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0270
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5440

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
F 369 ASN
** F 412 ASN ** 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 = 0.3596 r_free = 0.3596 target = 0.112015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.092257 restraints weight = 8189.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.094714 restraints weight = 5100.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.096445 restraints weight = 3640.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3595  Z= 0.129
  Angle     :  0.617   8.603   4900  Z= 0.319
  Chirality :  0.045   0.197    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.544  35.180    496
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.18 (0.41), residues: 433
  helix:  2.39 (0.51), residues: 108
  sheet:  0.86 (0.43), residues: 127
  loop : -0.14 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP F 366 
 HIS   0.003   0.001   HIS B 465 
 PHE   0.012   0.001   PHE F 348 
 TYR   0.014   0.001   TYR A  82 
 ARG   0.001   0.000   ARG F 385 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00071 (    1)
  link_NAG-ASN         : angle       1.86685 (    3)
  hydrogen bonds       : bond        0.03580 (  159)
  hydrogen bonds       : angle       4.43021 (  474)
  SS BOND              : bond        0.00439 (    6)
  SS BOND              : angle       3.44595 (   12)
  covalent geometry    : bond        0.00299 ( 3588)
  covalent geometry    : angle       0.59256 ( 4885)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1798.29 seconds
wall clock time: 31 minutes 56.40 seconds (1916.40 seconds total)