Starting phenix.real_space_refine
on Thu Sep 10 20:09:33 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/09_2026/8dly_27520.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.032
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      13      5.16       5
     C    1582      2.51       5
     N     417      2.21       5
     O     471      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2483
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1546
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1546
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "H"
      Number of atoms: 923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 923
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.83, per 1000 atoms: 0.33
  Number of scatterers: 2483
  At special positions: 0
  Unit cell: (68, 82, 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      13     16.00
     O     471      8.00
     N     417      7.00
     C    1582      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " 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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.13
  Conformation dependent library (CDL) restraints added in 69.5 milliseconds
  

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  572

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 5 sheets defined
      13.4% alpha, 28.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 3.619A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 384 through 389
      removed outlier: 4.081A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.330A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.505A  pdb=" N   ASP H  89 " --> pdb=" O   ARG H  86 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 86 through 90'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.660A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.815A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.124A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   MET H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   ASN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    186 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: 0.35

  Time building geometry restraints manager: 0.19 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: 783
        1.34 -     1.46: 649
        1.46 -     1.58: 1102
        1.58 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 2550
  Sorted by residual:
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.47e+00
  bond pdb=" CB  ASN H  50 "
       pdb=" CG  ASN H  50 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.38e+00
  bond pdb=" C   ALA C 520 "
       pdb=" N   PRO C 521 "
    ideal  model  delta    sigma   weight residual
    1.330  1.348 -0.018 1.19e-02 7.06e+03 2.32e+00
  bond pdb=" CB  GLU C 465 "
       pdb=" CG  GLU C 465 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.13e+00
  bond pdb=" CG  GLU C 465 "
       pdb=" CD  GLU C 465 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.71e+00
  ... (remaining 2545 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 3270
        1.92 -     3.84: 172
        3.84 -     5.76: 21
        5.76 -     7.68: 4
        7.68 -     9.60: 2
  Bond angle restraints: 3469
  Sorted by residual:
  angle pdb=" CB  GLU C 465 "
        pdb=" CG  GLU C 465 "
        pdb=" CD  GLU C 465 "
      ideal   model   delta    sigma   weight residual
     112.60  118.87   -6.27 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" C   GLY C 476 "
        pdb=" N   SER C 477 "
        pdb=" CA  SER C 477 "
      ideal   model   delta    sigma   weight residual
     121.54  127.51   -5.97 1.91e+00 2.74e-01 9.78e+00
  angle pdb=" C   VAL C 483 "
        pdb=" N   GLU C 484 "
        pdb=" CA  GLU C 484 "
      ideal   model   delta    sigma   weight residual
     120.38  124.48   -4.10 1.37e+00 5.33e-01 8.95e+00
  angle pdb=" N   LEU C 518 "
        pdb=" CA  LEU C 518 "
        pdb=" C   LEU C 518 "
      ideal   model   delta    sigma   weight residual
     110.80  117.14   -6.34 2.13e+00 2.20e-01 8.87e+00
  angle pdb=" CA  LEU H  63 "
        pdb=" CB  LEU H  63 "
        pdb=" CG  LEU H  63 "
      ideal   model   delta    sigma   weight residual
     116.30  125.90   -9.60 3.50e+00 8.16e-02 7.52e+00
  ... (remaining 3464 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.75: 1289
       13.75 -    27.50: 144
       27.50 -    41.25: 36
       41.25 -    54.99: 9
       54.99 -    68.74: 1
  Dihedral angle restraints: 1479
    sinusoidal: 572
      harmonic: 907
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.09  -33.09     1      1.00e+01 1.00e-02 1.56e+01
  dihedral pdb=" CA  ASN C 487 "
           pdb=" C   ASN C 487 "
           pdb=" N   CYS C 488 "
           pdb=" CA  CYS C 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.29  -15.71     0      5.00e+00 4.00e-02 9.87e+00
  dihedral pdb=" CG  ARG C 509 "
           pdb=" CD  ARG C 509 "
           pdb=" NE  ARG C 509 "
           pdb=" CZ  ARG C 509 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.99   41.99     2      1.50e+01 4.44e-03 9.55e+00
  ... (remaining 1476 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 224
       0.046 -    0.093: 100
       0.093 -    0.139: 38
       0.139 -    0.185: 5
       0.185 -    0.231: 3
  Chirality restraints: 370
  Sorted by residual:
  chirality pdb=" CB  THR C 470 "
            pdb=" CA  THR C 470 "
            pdb=" OG1 THR C 470 "
            pdb=" CG2 THR C 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  MET H 106 "
            pdb=" N   MET H 106 "
            pdb=" C   MET H 106 "
            pdb=" CB  MET H 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL H  37 "
            pdb=" N   VAL H  37 "
            pdb=" C   VAL H  37 "
            pdb=" CB  VAL H  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 367 not shown)

  Planarity restraints: 449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 520 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" C   ALA C 520 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA C 520 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   PRO C 521 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN H  60 "    0.035 5.00e-02 4.00e+02   5.30e-02 4.49e+00
        pdb=" N   PRO H  61 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO H  61 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H  61 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H  40 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO H  41 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "    0.025 5.00e-02 4.00e+02
  ... (remaining 446 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 789
        2.83 -     3.35: 1927
        3.35 -     3.87: 4036
        3.87 -     4.38: 4493
        4.38 -     4.90: 8057
  Nonbonded interactions: 19302
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 450 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" NE  ARG C 457 "
            pdb=" OD2 ASP C 467 "
     model   vdw
     2.432 3.120
  nonbonded pdb=" O   ILE C 418 "
            pdb=" N   TYR C 423 "
     model   vdw
     2.487 3.120
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.505 3.040
  nonbonded pdb=" O4  NAG C1301 "
            pdb=" O6  NAG C1301 "
     model   vdw
     2.524 3.040
  ... (remaining 19297 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.360
  Find NCS groups from input model:        0.010
  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:5.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
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   0.051   2556  Z= 0.237
  Angle     :  0.945   9.601   3482  Z= 0.513
  Chirality :  0.059   0.231    370
  Planarity :  0.006   0.053    448
  Dihedral  : 12.370  68.742    892
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.00 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.40), residues: 310
  helix: -3.94 (0.60), residues: 26
  sheet: -0.08 (0.45), residues: 104
  loop : -1.03 (0.37), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  97 
 TYR   0.015   0.002   TYR C 453 
 PHE   0.017   0.002   PHE H  27 
 TRP   0.021   0.003   TRP H  47 
 HIS   0.011   0.003   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00521 /  0.24 ( 2550)
  covalent geometry    : angle       0.93943 /  0.51 ( 3469)
  SS BOND              : bond        0.00516 /  0.27 (    5)
  SS BOND              : angle       1.21448 /  0.70 (   10)
  hydrogen bonds       : bond        0.13741 /  8.09 (   74)
  hydrogen bonds       : angle       9.45269 /  6.47 (  186)
  link_NAG-ASN         : bond        0.00546 /  0.29 (    1)
  link_NAG-ASN         : angle       3.46937 /  1.86 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.094 
Fit side-chains
REVERT: C  420 ASP cc_start: 0.8523 (m-30) cc_final: 0.8208 (m-30)
REVERT: C  424 LYS cc_start: 0.8837 (tptt) cc_final: 0.8592 (tppp)
REVERT: C  456 PHE cc_start: 0.8662 (t80) cc_final: 0.8216 (t80)
REVERT: C  474 GLN cc_start: 0.7635 (mt0) cc_final: 0.7418 (mt0)
REVERT: H   39 GLN cc_start: 0.7731 (pt0) cc_final: 0.7150 (pm20)
REVERT: H   52 TYR cc_start: 0.8889 (m-80) cc_final: 0.8688 (m-80)
REVERT: H   86 ARG cc_start: 0.6993 (mtp180) cc_final: 0.6617 (mtp180)
REVERT: H   92 ILE cc_start: 0.8543 (mt) cc_final: 0.7761 (mm)
  outliers start: 1
  outliers final: 2
  residues processed: 100
  average time/residue: 0.5221
  time to fit residues: 53.3481
Evaluate side-chains
  64 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   54 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 474 GLN
C 506 GLN
** H  76 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 = 0.3417 r_free = 0.3417 target = 0.086884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.074686 restraints weight = 6008.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 3.19
r_work: 0.3074 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2556  Z= 0.181
  Angle     :  0.622   6.449   3482  Z= 0.313
  Chirality :  0.045   0.147    370
  Planarity :  0.005   0.032    448
  Dihedral  :  8.717 126.088    356
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.85 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.42), residues: 310
  helix: -3.44 (0.78), residues: 27
  sheet:  0.04 (0.48), residues: 98
  loop : -0.69 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  16 
 TYR   0.015   0.001   TYR H  79 
 PHE   0.008   0.001   PHE C 347 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.003   0.001   HIS C 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 ( 2550)
  covalent geometry    : angle       0.62049 /  0.31 ( 3469)
  SS BOND              : bond        0.00446 /  0.23 (    5)
  SS BOND              : angle       0.72564 /  0.42 (   10)
  hydrogen bonds       : bond        0.03457 /  2.21 (   74)
  hydrogen bonds       : angle       7.34086 /  5.02 (  186)
  link_NAG-ASN         : bond        0.00337 /  0.18 (    1)
  link_NAG-ASN         : angle       1.52870 /  0.82 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8702 (m-30) cc_final: 0.8448 (m-30)
REVERT: C  424 LYS cc_start: 0.8982 (tptt) cc_final: 0.8706 (tppp)
REVERT: H   29 PHE cc_start: 0.8630 (t80) cc_final: 0.8203 (t80)
REVERT: H   60 ASN cc_start: 0.9066 (t0) cc_final: 0.8836 (t0)
REVERT: H   86 ARG cc_start: 0.7445 (mtp180) cc_final: 0.6657 (mtp180)
  outliers start: 11
  outliers final: 6
  residues processed: 77
  average time/residue: 0.5581
  time to fit residues: 43.8881
Evaluate side-chains
  68 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   27 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0980
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.083969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.071886 restraints weight = 6075.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 3.14
r_work: 0.3019 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2556  Z= 0.178
  Angle     :  0.596   6.388   3482  Z= 0.302
  Chirality :  0.045   0.138    370
  Planarity :  0.004   0.031    448
  Dihedral  :  5.467  47.703    354
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 17.98 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.43), residues: 310
  helix: -3.32 (1.13), residues: 20
  sheet: -0.11 (0.47), residues: 103
  loop : -0.80 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  16 
 TYR   0.011   0.001   TYR H  79 
 PHE   0.013   0.001   PHE H  29 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 ( 2550)
  covalent geometry    : angle       0.59454 /  0.30 ( 3469)
  SS BOND              : bond        0.00247 /  0.12 (    5)
  SS BOND              : angle       0.63585 /  0.37 (   10)
  hydrogen bonds       : bond        0.03057 /  1.89 (   74)
  hydrogen bonds       : angle       7.02202 /  4.80 (  186)
  link_NAG-ASN         : bond        0.00284 /  0.15 (    1)
  link_NAG-ASN         : angle       1.46037 /  0.80 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8682 (m-30) cc_final: 0.8402 (m-30)
REVERT: C  424 LYS cc_start: 0.9080 (tptt) cc_final: 0.8842 (tppp)
REVERT: C  444 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8169 (mtmm)
REVERT: H   60 ASN cc_start: 0.9020 (t0) cc_final: 0.8807 (t0)
REVERT: H   86 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6758 (mtp180)
REVERT: H   88 GLU cc_start: 0.9033 (pp20) cc_final: 0.8691 (pp20)
REVERT: H   89 ASP cc_start: 0.8157 (m-30) cc_final: 0.7861 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 76
  average time/residue: 0.5248
  time to fit residues: 40.8043
Evaluate side-chains
  71 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0070
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.086251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.074013 restraints weight = 5913.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 3.26
r_work: 0.3071 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2556  Z= 0.134
  Angle     :  0.564   6.877   3482  Z= 0.284
  Chirality :  0.043   0.134    370
  Planarity :  0.004   0.034    448
  Dihedral  :  5.065  43.955    352
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 19.85 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.44), residues: 310
  helix: -3.31 (1.12), residues: 20
  sheet: -0.05 (0.46), residues: 110
  loop : -0.70 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.009   0.001   TYR H  79 
 PHE   0.006   0.001   PHE C 347 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 2550)
  covalent geometry    : angle       0.56280 /  0.28 ( 3469)
  SS BOND              : bond        0.00191 /  0.11 (    5)
  SS BOND              : angle       0.44469 /  0.26 (   10)
  hydrogen bonds       : bond        0.02667 /  1.65 (   74)
  hydrogen bonds       : angle       6.74953 /  4.64 (  186)
  link_NAG-ASN         : bond        0.00264 /  0.14 (    1)
  link_NAG-ASN         : angle       1.33623 /  0.74 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8632 (m-30) cc_final: 0.8360 (m-30)
REVERT: C  424 LYS cc_start: 0.8984 (tptt) cc_final: 0.8707 (tppp)
REVERT: C  444 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8080 (mtmm)
REVERT: H   29 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7388 (t80)
REVERT: H   54 ASP cc_start: 0.8934 (t0) cc_final: 0.8723 (p0)
REVERT: H   60 ASN cc_start: 0.8982 (t0) cc_final: 0.8775 (t0)
REVERT: H   74 SER cc_start: 0.9217 (m) cc_final: 0.8950 (t)
REVERT: H   82 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8174 (mtp)
REVERT: H   86 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6686 (mtp180)
REVERT: H   88 GLU cc_start: 0.9074 (pp20) cc_final: 0.8647 (pp20)
REVERT: H   89 ASP cc_start: 0.8130 (m-30) cc_final: 0.7817 (m-30)
  outliers start: 14
  outliers final: 5
  residues processed: 77
  average time/residue: 0.5488
  time to fit residues: 43.1830
Evaluate side-chains
  75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   29 PHE
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  113 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.086119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.073747 restraints weight = 5897.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 3.25
r_work: 0.3052 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2556  Z= 0.161
  Angle     :  0.570   6.189   3482  Z= 0.288
  Chirality :  0.043   0.135    370
  Planarity :  0.004   0.033    448
  Dihedral  :  5.043  44.611    352
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 20.22 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.44), residues: 310
  helix: -3.23 (1.13), residues: 20
  sheet: -0.13 (0.49), residues: 98
  loop : -0.66 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.013   0.001   TYR H 101 
 PHE   0.007   0.001   PHE C 347 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 2550)
  covalent geometry    : angle       0.56872 /  0.29 ( 3469)
  SS BOND              : bond        0.00226 /  0.12 (    5)
  SS BOND              : angle       0.41842 /  0.25 (   10)
  hydrogen bonds       : bond        0.02645 /  1.63 (   74)
  hydrogen bonds       : angle       6.51485 /  4.51 (  186)
  link_NAG-ASN         : bond        0.00237 /  0.12 (    1)
  link_NAG-ASN         : angle       1.42810 /  0.79 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8659 (m-30) cc_final: 0.8370 (m-30)
REVERT: C  424 LYS cc_start: 0.9007 (tptt) cc_final: 0.8677 (tppp)
REVERT: C  444 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8139 (mtmm)
REVERT: H   39 GLN cc_start: 0.8076 (pt0) cc_final: 0.7610 (tt0)
REVERT: H   60 ASN cc_start: 0.8999 (t0) cc_final: 0.8771 (t0)
REVERT: H   74 SER cc_start: 0.9238 (m) cc_final: 0.8964 (t)
REVERT: H   82 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8257 (mtp)
REVERT: H   86 ARG cc_start: 0.7284 (mtp180) cc_final: 0.6629 (mtp180)
REVERT: H   88 GLU cc_start: 0.9053 (pp20) cc_final: 0.8612 (pp20)
  outliers start: 19
  outliers final: 9
  residues processed: 81
  average time/residue: 0.5165
  time to fit residues: 42.8452
Evaluate side-chains
  78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   82 MET
Chi-restraints excluded: chain H residue  113 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    0.0050
   chunk 21 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0060
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4810

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 474 GLN
C 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.087137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.074778 restraints weight = 5862.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.21
r_work: 0.3082 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2556  Z= 0.121
  Angle     :  0.593   9.418   3482  Z= 0.289
  Chirality :  0.044   0.133    370
  Planarity :  0.004   0.035    448
  Dihedral  :  4.784  40.310    352
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 22.47 %
    Favored  : 72.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.44), residues: 310
  helix: -3.32 (1.03), residues: 20
  sheet: -0.02 (0.51), residues: 92
  loop : -0.51 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.008   0.001   TYR C 495 
 PHE   0.005   0.001   PHE C 347 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 2550)
  covalent geometry    : angle       0.59253 /  0.29 ( 3469)
  SS BOND              : bond        0.00178 /  0.10 (    5)
  SS BOND              : angle       0.53509 /  0.28 (   10)
  hydrogen bonds       : bond        0.02456 /  1.54 (   74)
  hydrogen bonds       : angle       6.42063 /  4.46 (  186)
  link_NAG-ASN         : bond        0.00240 /  0.13 (    1)
  link_NAG-ASN         : angle       1.29748 /  0.72 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8967 (ttm-80) cc_final: 0.8522 (tmm-80)
REVERT: C  420 ASP cc_start: 0.8625 (m-30) cc_final: 0.8345 (m-30)
REVERT: C  424 LYS cc_start: 0.8959 (tptt) cc_final: 0.8692 (tppp)
REVERT: C  444 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8147 (mtmm)
REVERT: C  516 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: H   39 GLN cc_start: 0.8058 (pt0) cc_final: 0.7628 (tt0)
REVERT: H   50 ASN cc_start: 0.7864 (t0) cc_final: 0.7651 (t0)
REVERT: H   60 ASN cc_start: 0.8978 (t0) cc_final: 0.8760 (t0)
REVERT: H   74 SER cc_start: 0.9205 (m) cc_final: 0.8936 (t)
REVERT: H   82 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (mtp)
REVERT: H   86 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6599 (mtp180)
REVERT: H   88 GLU cc_start: 0.9105 (pp20) cc_final: 0.8612 (pp20)
REVERT: H   89 ASP cc_start: 0.8122 (m-30) cc_final: 0.7846 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 75
  average time/residue: 0.5969
  time to fit residues: 45.6374
Evaluate side-chains
  72 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   82 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0010
   chunk 1 optimal weight:    0.0870
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0670
   chunk 27 optimal weight:    0.0170
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.1740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.089732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.077229 restraints weight = 5836.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 3.25
r_work: 0.3108 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   2556  Z= 0.100
  Angle     :  0.573   8.246   3482  Z= 0.282
  Chirality :  0.043   0.133    370
  Planarity :  0.004   0.035    448
  Dihedral  :  4.276  31.538    352
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 23.60 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.45), residues: 310
  helix: -3.30 (1.00), residues: 20
  sheet:  0.20 (0.52), residues: 90
  loop : -0.53 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.006   0.001   TYR H  79 
 PHE   0.006   0.001   PHE C 392 
 TRP   0.008   0.001   TRP C 436 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.10 ( 2550)
  covalent geometry    : angle       0.57192 /  0.28 ( 3469)
  SS BOND              : bond        0.00143 /  0.10 (    5)
  SS BOND              : angle       0.55375 /  0.30 (   10)
  hydrogen bonds       : bond        0.02218 /  1.38 (   74)
  hydrogen bonds       : angle       6.14839 /  4.29 (  186)
  link_NAG-ASN         : bond        0.00266 /  0.14 (    1)
  link_NAG-ASN         : angle       1.13072 /  0.64 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.9001 (ttm-80) cc_final: 0.8537 (tmm-80)
REVERT: C  408 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8419 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8631 (m-30) cc_final: 0.8388 (m-30)
REVERT: C  424 LYS cc_start: 0.8976 (tptt) cc_final: 0.8715 (tppp)
REVERT: C  444 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8149 (mtmm)
REVERT: C  516 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6567 (tm-30)
REVERT: C  517 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7525 (tm)
REVERT: H    3 GLN cc_start: 0.8012 (tp40) cc_final: 0.7299 (mp10)
REVERT: H   39 GLN cc_start: 0.8065 (pt0) cc_final: 0.7674 (tt0)
REVERT: H   60 ASN cc_start: 0.8834 (t0) cc_final: 0.8429 (t0)
REVERT: H   74 SER cc_start: 0.9158 (m) cc_final: 0.8913 (t)
REVERT: H   82 MET cc_start: 0.8557 (mtm) cc_final: 0.8205 (mtp)
REVERT: H   86 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6740 (mtp-110)
REVERT: H   88 GLU cc_start: 0.9115 (pp20) cc_final: 0.8592 (pp20)
REVERT: H   89 ASP cc_start: 0.7902 (m-30) cc_final: 0.7680 (m-30)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.5810
  time to fit residues: 50.4280
Evaluate side-chains
  70 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   27 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0980
   chunk 18 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.4957 > 50:)
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.088348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.075859 restraints weight = 5911.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 3.20
r_work: 0.3083 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2556  Z= 0.136
  Angle     :  0.608   8.516   3482  Z= 0.294
  Chirality :  0.044   0.171    370
  Planarity :  0.004   0.038    448
  Dihedral  :  4.413  33.928    352
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.22 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.45), residues: 310
  helix: -3.06 (1.09), residues: 20
  sheet:  0.41 (0.55), residues: 83
  loop : -0.57 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  16 
 TYR   0.010   0.001   TYR H  32 
 PHE   0.023   0.001   PHE H  27 
 TRP   0.009   0.001   TRP H  36 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 2550)
  covalent geometry    : angle       0.60697 /  0.29 ( 3469)
  SS BOND              : bond        0.00203 /  0.11 (    5)
  SS BOND              : angle       0.46927 /  0.26 (   10)
  hydrogen bonds       : bond        0.02395 /  1.52 (   74)
  hydrogen bonds       : angle       6.16516 /  4.29 (  186)
  link_NAG-ASN         : bond        0.00222 /  0.12 (    1)
  link_NAG-ASN         : angle       1.27207 /  0.71 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8497 (tmm-80)
REVERT: C  420 ASP cc_start: 0.8623 (m-30) cc_final: 0.8406 (m-30)
REVERT: C  424 LYS cc_start: 0.8990 (tptt) cc_final: 0.8653 (tppp)
REVERT: C  444 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8180 (mtmm)
REVERT: C  516 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6978 (tm-30)
REVERT: C  517 LEU cc_start: 0.7783 (mm) cc_final: 0.7513 (tm)
REVERT: H   39 GLN cc_start: 0.8096 (pt0) cc_final: 0.7699 (tt0)
REVERT: H   50 ASN cc_start: 0.7850 (t0) cc_final: 0.7590 (t0)
REVERT: H   60 ASN cc_start: 0.8917 (t0) cc_final: 0.8489 (t0)
REVERT: H   74 SER cc_start: 0.9181 (m) cc_final: 0.8920 (t)
REVERT: H   82 MET cc_start: 0.8607 (mtm) cc_final: 0.8255 (mtp)
REVERT: H   86 ARG cc_start: 0.7349 (mtp180) cc_final: 0.6681 (mtp180)
REVERT: H   88 GLU cc_start: 0.9081 (pp20) cc_final: 0.8599 (pp20)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.5381
  time to fit residues: 41.2571
Evaluate side-chains
  74 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.086770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.074160 restraints weight = 6030.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 3.26
r_work: 0.3061 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2556  Z= 0.161
  Angle     :  0.626   8.174   3482  Z= 0.304
  Chirality :  0.045   0.158    370
  Planarity :  0.004   0.038    448
  Dihedral  :  4.766  42.080    352
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.47 %
    Favored  : 69.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.45), residues: 310
  helix: -2.91 (1.15), residues: 20
  sheet:  0.37 (0.55), residues: 83
  loop : -0.62 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.012   0.001   TYR H  52 
 PHE   0.007   0.001   PHE H  27 
 TRP   0.009   0.001   TRP H  36 
 HIS   0.002   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 2550)
  covalent geometry    : angle       0.62567 /  0.30 ( 3469)
  SS BOND              : bond        0.00210 /  0.10 (    5)
  SS BOND              : angle       0.51166 /  0.28 (   10)
  hydrogen bonds       : bond        0.02517 /  1.58 (   74)
  hydrogen bonds       : angle       6.25743 /  4.34 (  186)
  link_NAG-ASN         : bond        0.00211 /  0.11 (    1)
  link_NAG-ASN         : angle       1.36325 /  0.75 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8956 (ttm-80) cc_final: 0.8361 (tmm-80)
REVERT: C  408 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8494 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8984 (tptt) cc_final: 0.8657 (tppp)
REVERT: C  444 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8122 (mtmm)
REVERT: C  516 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6702 (tm-30)
REVERT: H   39 GLN cc_start: 0.8106 (pt0) cc_final: 0.7631 (tt0)
REVERT: H   60 ASN cc_start: 0.9006 (t0) cc_final: 0.8526 (t0)
REVERT: H   74 SER cc_start: 0.9177 (m) cc_final: 0.8912 (t)
REVERT: H   86 ARG cc_start: 0.7455 (mtp180) cc_final: 0.6773 (mtp180)
REVERT: H   88 GLU cc_start: 0.9083 (pp20) cc_final: 0.8591 (pp20)
REVERT: H   89 ASP cc_start: 0.8149 (m-30) cc_final: 0.7857 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 72
  average time/residue: 0.5230
  time to fit residues: 38.5040
Evaluate side-chains
  73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    0.2980
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0770
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 506 GLN
** H  50 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 = 0.3427 r_free = 0.3427 target = 0.087541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.074879 restraints weight = 6046.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 3.27
r_work: 0.3073 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2556  Z= 0.132
  Angle     :  0.628   8.974   3482  Z= 0.304
  Chirality :  0.044   0.153    370
  Planarity :  0.004   0.036    448
  Dihedral  :  4.643  39.732    352
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 27.34 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.45), residues: 310
  helix: -2.89 (1.15), residues: 20
  sheet:  0.28 (0.55), residues: 83
  loop : -0.63 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  16 
 TYR   0.013   0.001   TYR H  52 
 PHE   0.005   0.001   PHE C 515 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.13 ( 2550)
  covalent geometry    : angle       0.62718 /  0.30 ( 3469)
  SS BOND              : bond        0.00161 /  0.08 (    5)
  SS BOND              : angle       0.52729 /  0.30 (   10)
  hydrogen bonds       : bond        0.02476 /  1.56 (   74)
  hydrogen bonds       : angle       6.13927 /  4.28 (  186)
  link_NAG-ASN         : bond        0.00239 /  0.13 (    1)
  link_NAG-ASN         : angle       1.28089 /  0.72 (    3)

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

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

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  620 Ramachandran restraints generated.
    310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8963 (ttm-80) cc_final: 0.8413 (tmm-80)
REVERT: C  408 ARG cc_start: 0.8724 (ptm-80) cc_final: 0.8510 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8964 (tptt) cc_final: 0.8629 (tppp)
REVERT: C  444 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8126 (mtmm)
REVERT: C  486 PHE cc_start: 0.5004 (t80) cc_final: 0.4476 (t80)
REVERT: C  516 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6743 (tm-30)
REVERT: C  517 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7070 (mm)
REVERT: H   39 GLN cc_start: 0.8125 (pt0) cc_final: 0.7644 (tt0)
REVERT: H   60 ASN cc_start: 0.8976 (t0) cc_final: 0.8506 (t0)
REVERT: H   74 SER cc_start: 0.9194 (m) cc_final: 0.8944 (t)
REVERT: H   82 MET cc_start: 0.8772 (mtm) cc_final: 0.8440 (mtp)
REVERT: H   86 ARG cc_start: 0.7435 (mtp180) cc_final: 0.6757 (mtp180)
REVERT: H   88 GLU cc_start: 0.9064 (pp20) cc_final: 0.8560 (pp20)
REVERT: H   89 ASP cc_start: 0.8114 (m-30) cc_final: 0.7893 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 70
  average time/residue: 0.5513
  time to fit residues: 39.4301
Evaluate side-chains
  73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  444 LYS
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  500 THR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** H  50 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 = 0.3424 r_free = 0.3424 target = 0.087403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.074784 restraints weight = 6026.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.25
r_work: 0.3075 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2556  Z= 0.138
  Angle     :  0.642   8.993   3482  Z= 0.313
  Chirality :  0.044   0.149    370
  Planarity :  0.004   0.036    448
  Dihedral  :  4.587  39.020    352
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 27.34 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.45), residues: 310
  helix: -2.85 (1.16), residues: 20
  sheet:  0.20 (0.55), residues: 85
  loop : -0.61 (0.40), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  16 
 TYR   0.013   0.001   TYR H  52 
 PHE   0.005   0.001   PHE C 515 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 2550)
  covalent geometry    : angle       0.64171 /  0.31 ( 3469)
  SS BOND              : bond        0.00189 /  0.11 (    5)
  SS BOND              : angle       0.46315 /  0.26 (   10)
  hydrogen bonds       : bond        0.02448 /  1.56 (   74)
  hydrogen bonds       : angle       6.14269 /  4.27 (  186)
  link_NAG-ASN         : bond        0.00236 /  0.12 (    1)
  link_NAG-ASN         : angle       1.29778 /  0.72 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.88 seconds
wall clock time: 22 minutes 47.31 seconds (1367.31 seconds total)