Starting phenix.real_space_refine
on Wed Jun  4 15:56:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wp5_32669/06_2025/7wp5_32669.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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      15      5.16       5
     C    2118      2.51       5
     N     563      2.21       5
     O     644      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3340
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "L"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 811
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1017
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 128}
    Chain: "F"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1484
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 10, 'TRANS': 172}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.64, per 1000 atoms: 1.69
  Number of scatterers: 3340
  At special positions: 0
  Unit cell: (77.022, 80.912, 81.69, 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      15     16.00
     O     644      8.00
     N     563      7.00
     C    2118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 379 " - pdb=" SG  CYS F 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN F 343 "
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 394.0 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 7 sheets defined
      2.4% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'F' and resid 336 through 340
      removed outlier: 3.688A  pdb=" N   ASP F 339 " --> pdb=" O   CYS F 336 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLU F 340 " --> pdb=" O   PRO F 337 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 336 through 340'
    Processing helix  chain 'F' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'L' and resid 17 through 23
      removed outlier: 3.750A  pdb=" N   SER L  74 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 50
      removed outlier: 5.740A  pdb=" N   LEU L  48 " --> pdb=" O   GLN L  39 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   GLN L  39 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.600A  pdb=" N   VAL H   5 " --> pdb=" O   ALA H  23 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.618A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 126 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR H 125 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL H  50 " --> pdb=" O   TYR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 103 through 104
      removed outlier: 3.606A  pdb=" N   TYR H 103 " --> pdb=" O   ASN H 111 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ASN H 111 " --> pdb=" O   TYR H 103 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 358 through 359
      removed outlier: 3.735A  pdb=" N   VAL F 395 " --> pdb=" O   ILE F 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 376 through 379
      removed outlier: 3.527A  pdb=" N   THR F 376 " --> pdb=" O   ALA F 435 " (cutoff:3.500A)

    63 hydrogen bonds defined for protein.
    153 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: 0.70

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1052
        1.34 -     1.46: 852
        1.46 -     1.58: 1503
        1.58 -     1.70: 0
        1.70 -     1.82: 19
  Bond restraints: 3426
  Sorted by residual:
  bond pdb=" CA  SER F 446 "
       pdb=" C   SER F 446 "
    ideal  model  delta    sigma   weight residual
    1.522  1.544 -0.022 1.37e-02 5.33e+03 2.59e+00
  bond pdb=" CA  CYS F 336 "
       pdb=" C   CYS F 336 "
    ideal  model  delta    sigma   weight residual
    1.525  1.557 -0.032 2.10e-02 2.27e+03 2.31e+00
  bond pdb=" C3  NAG A   1 "
       pdb=" O3  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C3  NAG A   2 "
       pdb=" O3  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.431 -0.028 2.00e-02 2.50e+03 2.02e+00
  bond pdb=" C4  NAG A   1 "
       pdb=" O4  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.409  1.435 -0.026 2.00e-02 2.50e+03 1.75e+00
  ... (remaining 3421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 4522
        2.60 -     5.21: 110
        5.21 -     7.81: 17
        7.81 -    10.41: 1
       10.41 -    13.01: 4
  Bond angle restraints: 4654
  Sorted by residual:
  angle pdb=" C   ASN F 477 "
        pdb=" N   LYS F 478 "
        pdb=" CA  LYS F 478 "
      ideal   model   delta    sigma   weight residual
     121.80  132.91  -11.11 2.44e+00 1.68e-01 2.07e+01
  angle pdb=" C   GLY L  52 "
        pdb=" N   ASN L  53 "
        pdb=" CA  ASN L  53 "
      ideal   model   delta    sigma   weight residual
     121.54  130.03   -8.49 1.91e+00 2.74e-01 1.98e+01
  angle pdb=" C   TYR F 369 "
        pdb=" N   ASN F 370 "
        pdb=" CA  ASN F 370 "
      ideal   model   delta    sigma   weight residual
     122.19  128.42   -6.23 1.41e+00 5.03e-01 1.95e+01
  angle pdb=" C   SER F 359 "
        pdb=" N   ASN F 360 "
        pdb=" CA  ASN F 360 "
      ideal   model   delta    sigma   weight residual
     122.46  128.68   -6.22 1.41e+00 5.03e-01 1.95e+01
  angle pdb=" CA  LEU F 371 "
        pdb=" CB  LEU F 371 "
        pdb=" CG  LEU F 371 "
      ideal   model   delta    sigma   weight residual
     116.30  129.31  -13.01 3.50e+00 8.16e-02 1.38e+01
  ... (remaining 4649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.85: 1729
       14.85 -    29.70: 224
       29.70 -    44.55: 56
       44.55 -    59.41: 6
       59.41 -    74.26: 5
  Dihedral angle restraints: 2020
    sinusoidal: 800
      harmonic: 1220
  Sorted by residual:
  dihedral pdb=" CA  ASN F 460 "
           pdb=" C   ASN F 460 "
           pdb=" N   LEU F 461 "
           pdb=" CA  LEU F 461 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -147.27  -32.73     0      5.00e+00 4.00e-02 4.29e+01
  dihedral pdb=" CA  ASN F 477 "
           pdb=" C   ASN F 477 "
           pdb=" N   LYS F 478 "
           pdb=" CA  LYS F 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.90  -24.10     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ASN H 115 "
           pdb=" C   ASN H 115 "
           pdb=" N   TYR H 116 "
           pdb=" CA  TYR H 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.61  -20.39     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 2017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 392
       0.066 -    0.132: 80
       0.132 -    0.198: 21
       0.198 -    0.264: 1
       0.264 -    0.329: 1
  Chirality restraints: 495
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN F 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.71e+00
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.37   -0.03 2.00e-02 2.50e+03 2.11e+00
  chirality pdb=" CB  THR H  91 "
            pdb=" CA  THR H  91 "
            pdb=" OG1 THR H  91 "
            pdb=" CG2 THR H  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 9.87e-01
  ... (remaining 492 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.278 2.00e-02 2.50e+03   2.38e-01 7.10e+02
        pdb=" C7  NAG A   1 "    0.061 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "    0.016 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.402 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.202 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "    0.028 2.00e-02 2.50e+03   2.34e-02 6.84e+00
        pdb=" C7  NAG A   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.021 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "   -0.037 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 411 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO F 412 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F 412 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO F 412 "    0.029 5.00e-02 4.00e+02
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 935
        2.80 -     3.33: 2725
        3.33 -     3.85: 5189
        3.85 -     4.38: 5630
        4.38 -     4.90: 9998
  Nonbonded interactions: 24477
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F 442 "
            pdb=" OH  TYR F 451 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD2 ASP F 398 "
            pdb=" OH  TYR F 423 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NE2 HIS L  36 "
            pdb=" O   ASN H 115 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" NE2 GLN L  39 "
            pdb=" OD1 ASP L  84 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OG  SER H 130 "
            pdb=" N   SER H 131 "
     model   vdw
     2.373 3.120
  ... (remaining 24472 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=0.00 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:             11.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     15.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
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      :  0.005   0.039   3431  Z= 0.250
  Angle     :  1.027  13.015   4666  Z= 0.561
  Chirality :  0.060   0.329    495
  Planarity :  0.012   0.238    603
  Dihedral  : 13.947  74.258   1245
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.07 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.64 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -4.27 (0.34), residues: 419
  helix: -5.34 (0.29), residues: 11
  sheet: -1.85 (0.43), residues: 135
  loop : -3.47 (0.29), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  47 
 HIS   0.005   0.002   HIS L  36 
 PHE   0.017   0.003   PHE F 515 
 TYR   0.018   0.002   TYR F 508 
 ARG   0.004   0.001   ARG L  56 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00320 (    1)
  link_NAG-ASN         : angle       2.42326 (    3)
  link_BETA1-4         : bond        0.00664 (    1)
  link_BETA1-4         : angle       1.18892 (    3)
  hydrogen bonds       : bond        0.30171 (   63)
  hydrogen bonds       : angle      11.42120 (  153)
  SS BOND              : bond        0.00438 (    3)
  SS BOND              : angle       0.69593 (    6)
  covalent geometry    : bond        0.00511 ( 3426)
  covalent geometry    : angle       1.02540 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8612 (tp) cc_final: 0.8356 (tt)
REVERT: H   51 MET cc_start: 0.8020 (ttp) cc_final: 0.7744 (ttm)
REVERT: F  339 ASP cc_start: 0.7344 (t70) cc_final: 0.6803 (t70)
REVERT: F  368 LEU cc_start: 0.8505 (mt) cc_final: 0.8287 (mt)
REVERT: F  406 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7872 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 113
  average time/residue: 0.1844
  time to fit residues: 24.6061
Evaluate side-chains
  83 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  497 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    0.2980
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0170
   chunk 11 optimal weight:    0.4980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
** L  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  81 GLN
H 115 ASN
F 417 ASN
F 450 ASN
F 474 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.171088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.154234 restraints weight = 6410.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.159569 restraints weight = 3787.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.160979 restraints weight = 1983.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3431  Z= 0.150
  Angle     :  0.742   8.376   4666  Z= 0.377
  Chirality :  0.047   0.205    495
  Planarity :  0.005   0.034    603
  Dihedral  :  6.639  38.674    522
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.31 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.33 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.36), residues: 419
  helix: -3.98 (1.09), residues: 13
  sheet: -1.47 (0.42), residues: 143
  loop : -3.16 (0.32), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.013   0.002   PHE F 374 
 TYR   0.022   0.001   TYR F 369 
 ARG   0.006   0.001   ARG F 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    1)
  link_NAG-ASN         : angle       2.18766 (    3)
  link_BETA1-4         : bond        0.00194 (    1)
  link_BETA1-4         : angle       1.18398 (    3)
  hydrogen bonds       : bond        0.05080 (   63)
  hydrogen bonds       : angle       8.02694 (  153)
  SS BOND              : bond        0.00496 (    3)
  SS BOND              : angle       1.93675 (    6)
  covalent geometry    : bond        0.00322 ( 3426)
  covalent geometry    : angle       0.73672 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   50 ILE cc_start: 0.8947 (mt) cc_final: 0.8679 (mm)
REVERT: L  108 LEU cc_start: 0.8536 (tp) cc_final: 0.8258 (tt)
REVERT: H   38 ARG cc_start: 0.8180 (ptt180) cc_final: 0.7940 (ptm-80)
REVERT: H   51 MET cc_start: 0.7755 (ttp) cc_final: 0.7361 (ttm)
REVERT: H  116 TYR cc_start: 0.8547 (m-80) cc_final: 0.8249 (m-80)
REVERT: F  365 TYR cc_start: 0.8178 (m-10) cc_final: 0.7923 (m-10)
REVERT: F  368 LEU cc_start: 0.8400 (mt) cc_final: 0.8140 (mt)
  outliers start: 11
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1376
  time to fit residues: 15.2275
Evaluate side-chains
  87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  497 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   overall best weight:    1.0922

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 115 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.165704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.150213 restraints weight = 6472.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.154456 restraints weight = 5115.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.156207 restraints weight = 2368.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3846
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3846 r_free = 0.3846    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3846 r_free = 0.3846    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3846
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3431  Z= 0.227
  Angle     :  0.775   8.006   4666  Z= 0.393
  Chirality :  0.049   0.187    495
  Planarity :  0.005   0.042    603
  Dihedral  :  6.807  30.969    522
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.46 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 19.33 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.37), residues: 419
  helix: -4.38 (0.82), residues: 13
  sheet: -1.38 (0.43), residues: 138
  loop : -3.16 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP L 100 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.002   PHE F 338 
 TYR   0.016   0.002   TYR F 369 
 ARG   0.005   0.001   ARG F 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00012 (    1)
  link_NAG-ASN         : angle       1.03806 (    3)
  link_BETA1-4         : bond        0.00155 (    1)
  link_BETA1-4         : angle       1.32815 (    3)
  hydrogen bonds       : bond        0.04187 (   63)
  hydrogen bonds       : angle       7.00672 (  153)
  SS BOND              : bond        0.00617 (    3)
  SS BOND              : angle       1.68586 (    6)
  covalent geometry    : bond        0.00500 ( 3426)
  covalent geometry    : angle       0.77220 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8613 (tp) cc_final: 0.8261 (tt)
REVERT: L  111 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7325 (mt)
REVERT: H   51 MET cc_start: 0.7791 (ttp) cc_final: 0.7450 (ttm)
REVERT: H  116 TYR cc_start: 0.8587 (m-80) cc_final: 0.8367 (m-80)
REVERT: F  365 TYR cc_start: 0.8136 (m-10) cc_final: 0.7899 (m-10)
REVERT: F  368 LEU cc_start: 0.8437 (mt) cc_final: 0.8220 (mt)
REVERT: F  406 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8594 (mm-30)
REVERT: F  425 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (mp)
  outliers start: 22
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1331
  time to fit residues: 15.6577
Evaluate side-chains
  96 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  127 VAL
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 115 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.165931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.150587 restraints weight = 6535.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.154857 restraints weight = 5054.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.156770 restraints weight = 2350.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3857 r_free = 0.3857    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3857 r_free = 0.3857    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3431  Z= 0.203
  Angle     :  0.747   7.762   4666  Z= 0.379
  Chirality :  0.047   0.175    495
  Planarity :  0.005   0.043    603
  Dihedral  :  6.383  26.133    520
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.98 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 21.57 %
    Favored  : 71.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.48 (0.37), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -1.15 (0.44), residues: 136
  loop : -3.06 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP F 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.002   PHE F 515 
 TYR   0.016   0.001   TYR F 369 
 ARG   0.005   0.001   ARG F 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00191 (    1)
  link_NAG-ASN         : angle       1.15014 (    3)
  link_BETA1-4         : bond        0.00377 (    1)
  link_BETA1-4         : angle       1.39007 (    3)
  hydrogen bonds       : bond        0.03885 (   63)
  hydrogen bonds       : angle       6.76417 (  153)
  SS BOND              : bond        0.00485 (    3)
  SS BOND              : angle       1.43189 (    6)
  covalent geometry    : bond        0.00453 ( 3426)
  covalent geometry    : angle       0.74437 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8561 (tp) cc_final: 0.8230 (tt)
REVERT: H   51 MET cc_start: 0.7818 (ttp) cc_final: 0.7555 (ttm)
REVERT: F  406 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: F  425 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: F  457 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7648 (ttt-90)
  outliers start: 24
  outliers final: 15
  residues processed: 99
  average time/residue: 0.1284
  time to fit residues: 15.9373
Evaluate side-chains
  97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
H 115 ASN
** F 409 GLN ** 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 = 0.3976 r_free = 0.3976 target = 0.166878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.151781 restraints weight = 6512.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.155985 restraints weight = 5033.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.158037 restraints weight = 2322.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3431  Z= 0.175
  Angle     :  0.722   7.701   4666  Z= 0.362
  Chirality :  0.046   0.135    495
  Planarity :  0.004   0.041    603
  Dihedral  :  7.075  50.563    520
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 11.22 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 23.81 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.38), residues: 419
  helix: -5.84 (0.27), residues: 5
  sheet: -1.07 (0.44), residues: 137
  loop : -2.95 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.011   0.002   PHE F 515 
 TYR   0.014   0.001   TYR F 369 
 ARG   0.005   0.001   ARG F 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00425 (    1)
  link_NAG-ASN         : angle       2.18106 (    3)
  link_BETA1-4         : bond        0.00629 (    1)
  link_BETA1-4         : angle       1.56738 (    3)
  hydrogen bonds       : bond        0.03604 (   63)
  hydrogen bonds       : angle       6.52703 (  153)
  SS BOND              : bond        0.00437 (    3)
  SS BOND              : angle       1.27837 (    6)
  covalent geometry    : bond        0.00389 ( 3426)
  covalent geometry    : angle       0.71868 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8538 (tp) cc_final: 0.8218 (tt)
REVERT: H   51 MET cc_start: 0.7690 (ttp) cc_final: 0.7456 (ttm)
REVERT: H  116 TYR cc_start: 0.8508 (m-80) cc_final: 0.8273 (m-80)
REVERT: F  365 TYR cc_start: 0.8102 (m-10) cc_final: 0.7851 (m-10)
REVERT: F  425 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: F  457 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7670 (ttt-90)
  outliers start: 22
  outliers final: 16
  residues processed: 97
  average time/residue: 0.1451
  time to fit residues: 17.3668
Evaluate side-chains
  98 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    0.1980
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
F 370 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 422 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 = 0.3971 r_free = 0.3971 target = 0.166268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.150711 restraints weight = 6739.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155106 restraints weight = 5141.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.157076 restraints weight = 2403.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3431  Z= 0.161
  Angle     :  0.709   7.662   4666  Z= 0.355
  Chirality :  0.046   0.135    495
  Planarity :  0.004   0.039    603
  Dihedral  :  6.658  42.025    520
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.50 %
    Favored  : 89.26 %
  Rotamer:
    Outliers :  7.28 %
    Allowed  : 24.65 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.38), residues: 419
  helix: -5.83 (0.27), residues: 5
  sheet: -0.95 (0.44), residues: 138
  loop : -2.88 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.010   0.002   PHE H  29 
 TYR   0.013   0.001   TYR F 369 
 ARG   0.006   0.001   ARG F 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00704 (    1)
  link_NAG-ASN         : angle       2.65475 (    3)
  link_BETA1-4         : bond        0.00951 (    1)
  link_BETA1-4         : angle       1.45734 (    3)
  hydrogen bonds       : bond        0.03542 (   63)
  hydrogen bonds       : angle       6.30627 (  153)
  SS BOND              : bond        0.00383 (    3)
  SS BOND              : angle       1.13963 (    6)
  covalent geometry    : bond        0.00361 ( 3426)
  covalent geometry    : angle       0.70465 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 85
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8538 (tp) cc_final: 0.8221 (tt)
REVERT: H   51 MET cc_start: 0.7596 (ttp) cc_final: 0.7290 (ttm)
REVERT: F  365 TYR cc_start: 0.8066 (m-10) cc_final: 0.7793 (m-10)
REVERT: F  406 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8697 (mm-30)
REVERT: F  425 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8351 (mp)
REVERT: F  457 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.7657 (ttt-90)
  outliers start: 26
  outliers final: 18
  residues processed: 97
  average time/residue: 0.1143
  time to fit residues: 14.2415
Evaluate side-chains
  100 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  115 ASN
Chi-restraints excluded: chain H residue  127 VAL
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.2980
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 422 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 = 0.3988 r_free = 0.3988 target = 0.167880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.152283 restraints weight = 6530.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.157093 restraints weight = 5254.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.158660 restraints weight = 2315.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3431  Z= 0.161
  Angle     :  0.698   7.659   4666  Z= 0.351
  Chirality :  0.045   0.136    495
  Planarity :  0.004   0.037    603
  Dihedral  :  6.445  35.310    520
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.26 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 25.77 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.38), residues: 419
  helix: -5.82 (0.27), residues: 5
  sheet: -0.90 (0.45), residues: 138
  loop : -2.82 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.025   0.002   PHE H  27 
 TYR   0.013   0.001   TYR F 369 
 ARG   0.004   0.000   ARG F 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       2.96237 (    3)
  link_BETA1-4         : bond        0.00996 (    1)
  link_BETA1-4         : angle       1.50306 (    3)
  hydrogen bonds       : bond        0.03348 (   63)
  hydrogen bonds       : angle       6.20301 (  153)
  SS BOND              : bond        0.00373 (    3)
  SS BOND              : angle       1.11437 (    6)
  covalent geometry    : bond        0.00359 ( 3426)
  covalent geometry    : angle       0.69256 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8520 (tp) cc_final: 0.8210 (tt)
REVERT: H   12 VAL cc_start: 0.6011 (t) cc_final: 0.5791 (m)
REVERT: H   38 ARG cc_start: 0.7987 (ptm-80) cc_final: 0.7581 (ptm160)
REVERT: H   46 GLU cc_start: 0.7663 (pt0) cc_final: 0.7394 (pt0)
REVERT: H   51 MET cc_start: 0.7595 (ttp) cc_final: 0.7292 (ttm)
REVERT: F  365 TYR cc_start: 0.8074 (m-10) cc_final: 0.7799 (m-10)
REVERT: F  406 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8549 (mm-30)
REVERT: F  425 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8324 (mp)
REVERT: F  457 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.7664 (ttt-90)
  outliers start: 22
  outliers final: 20
  residues processed: 92
  average time/residue: 0.1117
  time to fit residues: 13.1982
Evaluate side-chains
  100 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain H residue  127 VAL
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  362 VAL
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  470 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    0.1980
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0070
   chunk 16 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.170490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.154367 restraints weight = 6569.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.159406 restraints weight = 4224.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.160875 restraints weight = 2282.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3431  Z= 0.115
  Angle     :  0.649   7.393   4666  Z= 0.326
  Chirality :  0.044   0.136    495
  Planarity :  0.004   0.032    603
  Dihedral  :  5.908  26.526    520
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.64 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 27.17 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.39), residues: 419
  helix: -5.64 (0.19), residues: 11
  sheet: -0.81 (0.45), residues: 139
  loop : -2.65 (0.34), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 436 
 HIS   0.001   0.001   HIS L  36 
 PHE   0.022   0.001   PHE H  27 
 TYR   0.013   0.001   TYR F 369 
 ARG   0.003   0.000   ARG F 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00247 (    1)
  link_NAG-ASN         : angle       3.16005 (    3)
  link_BETA1-4         : bond        0.00678 (    1)
  link_BETA1-4         : angle       1.41033 (    3)
  hydrogen bonds       : bond        0.02915 (   63)
  hydrogen bonds       : angle       6.04350 (  153)
  SS BOND              : bond        0.00185 (    3)
  SS BOND              : angle       0.80047 (    6)
  covalent geometry    : bond        0.00256 ( 3426)
  covalent geometry    : angle       0.64304 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.403 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8393 (tp) cc_final: 0.8095 (tt)
REVERT: H   38 ARG cc_start: 0.7924 (ptm-80) cc_final: 0.7396 (ptm160)
REVERT: H   46 GLU cc_start: 0.7631 (pt0) cc_final: 0.7377 (pt0)
REVERT: H   51 MET cc_start: 0.7473 (ttp) cc_final: 0.7144 (ttm)
REVERT: F  365 TYR cc_start: 0.8053 (m-10) cc_final: 0.7792 (m-10)
REVERT: F  406 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8553 (mm-30)
REVERT: F  425 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (mp)
REVERT: F  465 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8544 (tm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1130
  time to fit residues: 13.3374
Evaluate side-chains
  93 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  495 TYR
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0270
   chunk 7 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.167821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.152900 restraints weight = 6550.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.157295 restraints weight = 4979.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.159156 restraints weight = 2182.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3431  Z= 0.142
  Angle     :  0.662   7.469   4666  Z= 0.333
  Chirality :  0.044   0.136    495
  Planarity :  0.004   0.037    603
  Dihedral  :  5.859  25.058    520
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.31 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 27.45 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.39), residues: 419
  helix: -5.83 (0.26), residues: 5
  sheet: -0.83 (0.45), residues: 139
  loop : -2.69 (0.34), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.024   0.002   PHE H  27 
 TYR   0.012   0.001   TYR H 114 
 ARG   0.010   0.001   ARG F 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00366 (    1)
  link_NAG-ASN         : angle       3.19925 (    3)
  link_BETA1-4         : bond        0.00766 (    1)
  link_BETA1-4         : angle       1.35586 (    3)
  hydrogen bonds       : bond        0.03279 (   63)
  hydrogen bonds       : angle       5.77182 (  153)
  SS BOND              : bond        0.00332 (    3)
  SS BOND              : angle       1.05493 (    6)
  covalent geometry    : bond        0.00316 ( 3426)
  covalent geometry    : angle       0.65583 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: L  108 LEU cc_start: 0.8463 (tp) cc_final: 0.8163 (tt)
REVERT: H   38 ARG cc_start: 0.8037 (ptm-80) cc_final: 0.7469 (ptm160)
REVERT: H   46 GLU cc_start: 0.7704 (pt0) cc_final: 0.7442 (pt0)
REVERT: H   51 MET cc_start: 0.7324 (ttp) cc_final: 0.7116 (ttp)
REVERT: F  365 TYR cc_start: 0.7971 (m-10) cc_final: 0.7716 (m-10)
REVERT: F  406 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8577 (mm-30)
REVERT: F  425 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (mp)
  outliers start: 17
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1068
  time to fit residues: 12.2994
Evaluate side-chains
  91 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  368 LEU
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.0670
   chunk 38 optimal weight:    0.0270
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.3976

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.169962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.153731 restraints weight = 6405.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.158731 restraints weight = 4080.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.160159 restraints weight = 2163.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3431  Z= 0.127
  Angle     :  0.663   7.282   4666  Z= 0.334
  Chirality :  0.045   0.153    495
  Planarity :  0.004   0.039    603
  Dihedral  :  5.718  24.960    520
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  8.35 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 27.73 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.39), residues: 419
  helix: -5.83 (0.26), residues: 5
  sheet: -0.79 (0.47), residues: 129
  loop : -2.54 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.024   0.002   PHE H  27 
 TYR   0.012   0.001   TYR F 451 
 ARG   0.009   0.001   ARG F 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00321 (    1)
  link_NAG-ASN         : angle       3.27391 (    3)
  link_BETA1-4         : bond        0.00751 (    1)
  link_BETA1-4         : angle       1.38212 (    3)
  hydrogen bonds       : bond        0.03003 (   63)
  hydrogen bonds       : angle       5.75945 (  153)
  SS BOND              : bond        0.00233 (    3)
  SS BOND              : angle       0.97062 (    6)
  covalent geometry    : bond        0.00283 ( 3426)
  covalent geometry    : angle       0.65628 ( 4654)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.385 
Fit side-chains
REVERT: L  108 LEU cc_start: 0.8437 (tp) cc_final: 0.8146 (tt)
REVERT: H   28 THR cc_start: 0.8290 (m) cc_final: 0.7983 (p)
REVERT: H   38 ARG cc_start: 0.8026 (ptm-80) cc_final: 0.7552 (ptm160)
REVERT: H   46 GLU cc_start: 0.7655 (pt0) cc_final: 0.7421 (pt0)
REVERT: H   51 MET cc_start: 0.7238 (ttp) cc_final: 0.7021 (ttp)
REVERT: F  365 TYR cc_start: 0.8049 (m-10) cc_final: 0.7759 (m-10)
REVERT: F  406 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: F  425 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8229 (mp)
REVERT: F  465 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8546 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1151
  time to fit residues: 12.5809
Evaluate side-chains
  87 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   19 THR
Chi-restraints excluded: chain L residue   23 THR
Chi-restraints excluded: chain L residue   53 ASN
Chi-restraints excluded: chain L residue  110 VAL
Chi-restraints excluded: chain H residue   53 PHE
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain F residue  401 VAL
Chi-restraints excluded: chain F residue  418 ILE
Chi-restraints excluded: chain F residue  425 LEU
Chi-restraints excluded: chain F residue  430 THR
Chi-restraints excluded: chain F residue  480 CYS
Chi-restraints excluded: chain F residue  506 GLN
Chi-restraints excluded: chain F residue  511 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0020
   chunk 27 optimal weight:    0.3980
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 38 optimal weight:    0.1980
   overall best weight:    0.3988

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

Flipped N/Q/H residues before XYZ refinement:
** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.170055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.155135 restraints weight = 6532.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.159271 restraints weight = 4962.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.161232 restraints weight = 2300.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.3745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3431  Z= 0.124
  Angle     :  0.655   7.309   4666  Z= 0.331
  Chirality :  0.045   0.148    495
  Planarity :  0.004   0.036    603
  Dihedral  :  5.601  25.267    520
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  9.55 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 28.01 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.39), residues: 419
  helix: -5.83 (0.26), residues: 5
  sheet: -0.73 (0.47), residues: 129
  loop : -2.48 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.023   0.001   PHE H  27 
 TYR   0.010   0.001   TYR F 369 
 ARG   0.008   0.001   ARG F 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00300 (    1)
  link_NAG-ASN         : angle       3.24301 (    3)
  link_BETA1-4         : bond        0.00766 (    1)
  link_BETA1-4         : angle       1.32573 (    3)
  hydrogen bonds       : bond        0.02932 (   63)
  hydrogen bonds       : angle       5.64098 (  153)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       1.05137 (    6)
  covalent geometry    : bond        0.00278 ( 3426)
  covalent geometry    : angle       0.64870 ( 4654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1885.53 seconds
wall clock time: 33 minutes 20.18 seconds (2000.18 seconds total)