Starting phenix.real_space_refine
on Tue Mar  3 11:05:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dly_27520/03_2026/8dly_27520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/03_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_27520/03_2026/8dly_27520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2026/8dly_27520.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_2026/8dly_27520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/03_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-dev-5986/lib/python3.9/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 dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.74, per 1000 atoms: 0.30
  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: 0.19
  Conformation dependent library (CDL) restraints added in 99.3 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: 0.09
  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: 0.32

  Time building geometry restraints manager: 0.26 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: 1306
       13.75 -    27.50: 146
       27.50 -    41.25: 38
       41.25 -    54.99: 9
       54.99 -    68.74: 1
  Dihedral angle restraints: 1500
    sinusoidal: 593
      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 1497 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:             2.030
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     3.930
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:6.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
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  : 12.405  68.742    913
  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
  covalent geometry    : bond        0.00521 ( 2550)
  covalent geometry    : angle       0.93943 ( 3469)
  SS BOND              : bond        0.00516 (    5)
  SS BOND              : angle       1.21448 (   10)
  hydrogen bonds       : bond        0.13741 (   74)
  hydrogen bonds       : angle       9.45269 (  186)
  link_NAG-ASN         : bond        0.00546 (    1)
  link_NAG-ASN         : angle       3.46937 (    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  : 0.059 
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: 0.5411
  time to fit residues: 55.1957
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  : 0.090 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.087089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.074862 restraints weight = 6000.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.19
r_work: 0.3071 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   2556  Z= 0.179
  Angle     :  0.624   6.518   3482  Z= 0.312
  Chirality :  0.044   0.147    370
  Planarity :  0.005   0.031    448
  Dihedral  :  8.942 126.375    377
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.64
  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: -1.09 (0.42), residues: 310
  helix: -3.50 (0.77), residues: 27
  sheet:  0.04 (0.48), residues: 98
  loop : -0.67 (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   0.007   0.001   PHE C 347 
 TRP   0.012   0.001   TRP H  47 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 2550)
  covalent geometry    : angle       0.62120 ( 3469)
  SS BOND              : bond        0.00320 (    5)
  SS BOND              : angle       0.73994 (   10)
  hydrogen bonds       : bond        0.03405 (   74)
  hydrogen bonds       : angle       7.31918 (  186)
  link_NAG-ASN         : bond        0.00312 (    1)
  link_NAG-ASN         : angle       2.08518 (    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  : 0.094 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8699 (m-30) cc_final: 0.8445 (m-30)
REVERT: C  424 LYS cc_start: 0.8987 (tptt) cc_final: 0.8713 (tppp)
REVERT: H   29 PHE cc_start: 0.8628 (t80) cc_final: 0.8198 (t80)
REVERT: H   60 ASN cc_start: 0.9073 (t0) cc_final: 0.8854 (t0)
REVERT: H   86 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6660 (mtp180)
  outliers start: 11
  outliers final: 6
  residues processed: 77
  average time/residue: 0.5774
  time to fit residues: 45.3054
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  : 0.064 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0670
   overall best weight:    0.5496

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.086495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.074362 restraints weight = 6087.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 3.17
r_work: 0.3056 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3196

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= 0.130
  Angle     :  0.572   6.347   3482  Z= 0.289
  Chirality :  0.044   0.135    370
  Planarity :  0.004   0.032    448
  Dihedral  :  5.309  44.406    375
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 17.98 %
    Favored  : 76.40 %
  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: -1.05 (0.42), residues: 310
  helix: -3.43 (1.09), residues: 20
  sheet:  0.03 (0.47), residues: 103
  loop : -0.77 (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   0.006   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
  covalent geometry    : bond        0.00299 ( 2550)
  covalent geometry    : angle       0.56919 ( 3469)
  SS BOND              : bond        0.00173 (    5)
  SS BOND              : angle       0.60363 (   10)
  hydrogen bonds       : bond        0.02888 (   74)
  hydrogen bonds       : angle       6.94889 (  186)
  link_NAG-ASN         : bond        0.00333 (    1)
  link_NAG-ASN         : angle       2.09305 (    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
  90 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8430 (m-30)
REVERT: C  424 LYS cc_start: 0.9104 (tptt) cc_final: 0.8877 (tppp)
REVERT: C  444 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8167 (mtmm)
REVERT: H   60 ASN cc_start: 0.8987 (t0) cc_final: 0.8773 (t0)
REVERT: H   86 ARG cc_start: 0.7529 (mtp180) cc_final: 0.6865 (mtp180)
REVERT: H   88 GLU cc_start: 0.9042 (pp20) cc_final: 0.8691 (pp20)
REVERT: H   89 ASP cc_start: 0.7955 (m-30) cc_final: 0.7727 (m-30)
  outliers start: 15
  outliers final: 5
  residues processed: 81
  average time/residue: 0.5195
  time to fit residues: 42.9032
Evaluate side-chains
  70 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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  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:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.085627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.073261 restraints weight = 5907.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 3.27
r_work: 0.3066 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
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      :  0.004   0.048   2556  Z= 0.173
  Angle     :  0.607   7.103   3482  Z= 0.301
  Chirality :  0.044   0.138    370
  Planarity :  0.004   0.034    448
  Dihedral  :  5.322  46.164    373
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 19.48 %
    Favored  : 74.53 %
  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: -1.06 (0.43), residues: 310
  helix: -3.27 (1.14), residues: 20
  sheet: -0.08 (0.47), residues: 105
  loop : -0.75 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 403 
 TYR   0.012   0.001   TYR H  79 
 PHE   0.008   0.001   PHE C 347 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 2550)
  covalent geometry    : angle       0.60430 ( 3469)
  SS BOND              : bond        0.00230 (    5)
  SS BOND              : angle       0.45981 (   10)
  hydrogen bonds       : bond        0.02785 (   74)
  hydrogen bonds       : angle       6.87853 (  186)
  link_NAG-ASN         : bond        0.00245 (    1)
  link_NAG-ASN         : angle       2.07827 (    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
  83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8674 (m-30) cc_final: 0.8416 (m-30)
REVERT: C  424 LYS cc_start: 0.9036 (tptt) cc_final: 0.8787 (tppp)
REVERT: C  444 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8179 (mtmm)
REVERT: H   29 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7404 (t80)
REVERT: H   39 GLN cc_start: 0.8032 (pt0) cc_final: 0.7745 (tt0)
REVERT: H   74 SER cc_start: 0.9237 (m) cc_final: 0.8956 (t)
REVERT: H   86 ARG cc_start: 0.7411 (mtp180) cc_final: 0.6741 (mtp180)
REVERT: H   88 GLU cc_start: 0.9044 (pp20) cc_final: 0.8651 (pp20)
REVERT: H   89 ASP cc_start: 0.8115 (m-30) cc_final: 0.7810 (m-30)
  outliers start: 16
  outliers final: 7
  residues processed: 76
  average time/residue: 0.5712
  time to fit residues: 44.2735
Evaluate side-chains
  80 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
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  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   29 PHE
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:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.084946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.072962 restraints weight = 5805.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 3.09
r_work: 0.3056 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2556  Z= 0.170
  Angle     :  0.606   8.228   3482  Z= 0.302
  Chirality :  0.044   0.135    370
  Planarity :  0.004   0.034    448
  Dihedral  :  5.214  45.599    373
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 20.97 %
    Favored  : 73.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.02 (0.44), residues: 310
  helix: -3.33 (1.09), residues: 20
  sheet: -0.10 (0.47), residues: 104
  loop : -0.66 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.010   0.001   TYR C 495 
 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
  covalent geometry    : bond        0.00393 ( 2550)
  covalent geometry    : angle       0.60373 ( 3469)
  SS BOND              : bond        0.00231 (    5)
  SS BOND              : angle       0.41871 (   10)
  hydrogen bonds       : bond        0.02703 (   74)
  hydrogen bonds       : angle       6.73705 (  186)
  link_NAG-ASN         : bond        0.00238 (    1)
  link_NAG-ASN         : angle       2.07579 (    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
  89 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8599 (m-30) cc_final: 0.8323 (m-30)
REVERT: C  424 LYS cc_start: 0.8952 (tptt) cc_final: 0.8616 (tppp)
REVERT: C  444 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8116 (mtmm)
REVERT: C  516 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6761 (tm-30)
REVERT: H   39 GLN cc_start: 0.8029 (pt0) cc_final: 0.7759 (tt0)
REVERT: H   60 ASN cc_start: 0.9063 (t0) cc_final: 0.8797 (t0)
REVERT: H   74 SER cc_start: 0.9260 (m) cc_final: 0.8984 (t)
REVERT: H   86 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6652 (mtp180)
REVERT: H   88 GLU cc_start: 0.9090 (pp20) cc_final: 0.8652 (pp20)
  outliers start: 15
  outliers final: 6
  residues processed: 83
  average time/residue: 0.5212
  time to fit residues: 44.1651
Evaluate side-chains
  73 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  378 LYS
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 H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0670
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3420 r_free = 0.3420 target = 0.086408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.074068 restraints weight = 5899.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 3.21
r_work: 0.3073 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2556  Z= 0.129
  Angle     :  0.578   5.956   3482  Z= 0.288
  Chirality :  0.043   0.133    370
  Planarity :  0.004   0.030    448
  Dihedral  :  4.972  42.109    373
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 22.85 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.96 (0.44), residues: 310
  helix: -3.24 (1.10), residues: 20
  sheet: -0.10 (0.51), residues: 92
  loop : -0.58 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 403 
 TYR   0.014   0.001   TYR H 101 
 PHE   0.005   0.001   PHE C 347 
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 2550)
  covalent geometry    : angle       0.57507 ( 3469)
  SS BOND              : bond        0.00211 (    5)
  SS BOND              : angle       0.60832 (   10)
  hydrogen bonds       : bond        0.02495 (   74)
  hydrogen bonds       : angle       6.57314 (  186)
  link_NAG-ASN         : bond        0.00251 (    1)
  link_NAG-ASN         : angle       1.89693 (    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
  88 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8722 (ttm-80)
REVERT: C  408 ARG cc_start: 0.8674 (ptm-80) cc_final: 0.8457 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8993 (tptt) cc_final: 0.8665 (tppp)
REVERT: C  444 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8142 (mtmm)
REVERT: C  516 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6625 (tm-30)
REVERT: H   39 GLN cc_start: 0.8054 (pt0) cc_final: 0.7810 (tt0)
REVERT: H   50 ASN cc_start: 0.7927 (t0) cc_final: 0.7710 (t0)
REVERT: H   60 ASN cc_start: 0.9049 (t0) cc_final: 0.8820 (t0)
REVERT: H   74 SER cc_start: 0.9253 (m) cc_final: 0.8992 (t)
REVERT: H   86 ARG cc_start: 0.7271 (mtp180) cc_final: 0.6674 (mtp180)
REVERT: H   88 GLU cc_start: 0.9085 (pp20) cc_final: 0.8610 (pp20)
REVERT: H   89 ASP cc_start: 0.8034 (m-30) cc_final: 0.7760 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 81
  average time/residue: 0.5504
  time to fit residues: 45.5243
Evaluate side-chains
  76 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  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  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  113 THR
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:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0070
   overall best weight:    0.9404

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.085232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.073030 restraints weight = 5875.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 3.19
r_work: 0.3043 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   2556  Z= 0.179
  Angle     :  0.626   6.336   3482  Z= 0.307
  Chirality :  0.045   0.137    370
  Planarity :  0.004   0.038    448
  Dihedral  :  5.134  44.886    373
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 23.97 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.14 (0.44), residues: 310
  helix: -2.97 (0.98), residues: 26
  sheet: -0.05 (0.54), residues: 85
  loop : -0.74 (0.40), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  16 
 TYR   0.010   0.001   TYR C 495 
 PHE   0.009   0.001   PHE H  29 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 2550)
  covalent geometry    : angle       0.62329 ( 3469)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.60032 (   10)
  hydrogen bonds       : bond        0.02660 (   74)
  hydrogen bonds       : angle       6.56692 (  186)
  link_NAG-ASN         : bond        0.00206 (    1)
  link_NAG-ASN         : angle       2.02469 (    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
  84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.056 
Fit side-chains
   revert: symmetry clash
REVERT: C  424 LYS cc_start: 0.8959 (tptt) cc_final: 0.8597 (tppp)
REVERT: C  444 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8128 (mtmm)
REVERT: C  516 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: H   12 VAL cc_start: 0.7529 (OUTLIER) cc_final: 0.7279 (p)
REVERT: H   29 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.8138 (t80)
REVERT: H   39 GLN cc_start: 0.8069 (pt0) cc_final: 0.7821 (tt0)
REVERT: H   50 ASN cc_start: 0.8012 (t0) cc_final: 0.7710 (t0)
REVERT: H   52 TYR cc_start: 0.8886 (m-80) cc_final: 0.8654 (m-80)
REVERT: H   60 ASN cc_start: 0.9083 (t0) cc_final: 0.8848 (t0)
REVERT: H   74 SER cc_start: 0.9263 (m) cc_final: 0.9016 (t)
REVERT: H   86 ARG cc_start: 0.7399 (mtp180) cc_final: 0.6738 (mtp180)
REVERT: H   88 GLU cc_start: 0.9083 (pp20) cc_final: 0.8623 (pp20)
REVERT: H   89 ASP cc_start: 0.8187 (m-30) cc_final: 0.7883 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 75
  average time/residue: 0.5724
  time to fit residues: 43.7960
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
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   12 VAL
Chi-restraints excluded: chain H residue   29 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 7 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0770
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.3496

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.087796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.075647 restraints weight = 5938.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.13
r_work: 0.3091 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2556  Z= 0.110
  Angle     :  0.590   6.793   3482  Z= 0.287
  Chirality :  0.044   0.134    370
  Planarity :  0.004   0.040    448
  Dihedral  :  4.717  38.398    373
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 23.22 %
    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: -0.96 (0.44), residues: 310
  helix: -2.98 (1.15), residues: 20
  sheet:  0.05 (0.54), residues: 83
  loop : -0.68 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 403 
 TYR   0.013   0.001   TYR H 101 
 PHE   0.006   0.001   PHE H  29 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2550)
  covalent geometry    : angle       0.58818 ( 3469)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.51674 (   10)
  hydrogen bonds       : bond        0.02352 (   74)
  hydrogen bonds       : angle       6.32177 (  186)
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       1.72630 (    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
  88 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8686 (ptm-80) cc_final: 0.8443 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8510 (m-30) cc_final: 0.8132 (m-30)
REVERT: C  424 LYS cc_start: 0.8998 (tptt) cc_final: 0.8675 (tppp)
REVERT: C  444 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8153 (mtmm)
REVERT: C  516 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6968 (tm-30)
REVERT: C  517 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7404 (mm)
REVERT: H   39 GLN cc_start: 0.8037 (pt0) cc_final: 0.7793 (tt0)
REVERT: H   60 ASN cc_start: 0.9026 (t0) cc_final: 0.8794 (t0)
REVERT: H   74 SER cc_start: 0.9182 (m) cc_final: 0.8957 (t)
REVERT: H   86 ARG cc_start: 0.7312 (mtp180) cc_final: 0.6693 (mtp180)
REVERT: H   88 GLU cc_start: 0.9061 (pp20) cc_final: 0.8582 (pp20)
  outliers start: 15
  outliers final: 9
  residues processed: 81
  average time/residue: 0.5808
  time to fit residues: 48.0097
Evaluate side-chains
  77 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain H residue   27 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.087279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.074702 restraints weight = 6008.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.26
r_work: 0.3079 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4074

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= 0.153
  Angle     :  0.637   8.572   3482  Z= 0.311
  Chirality :  0.044   0.135    370
  Planarity :  0.004   0.033    448
  Dihedral  :  4.814  40.417    373
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 25.09 %
    Favored  : 70.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.92 (0.44), residues: 310
  helix: -2.98 (1.14), residues: 20
  sheet:  0.05 (0.54), residues: 83
  loop : -0.63 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  16 
 TYR   0.013   0.001   TYR H  52 
 PHE   0.019   0.001   PHE H  27 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 2550)
  covalent geometry    : angle       0.63534 ( 3469)
  SS BOND              : bond        0.00212 (    5)
  SS BOND              : angle       0.45841 (   10)
  hydrogen bonds       : bond        0.02534 (   74)
  hydrogen bonds       : angle       6.24731 (  186)
  link_NAG-ASN         : bond        0.00224 (    1)
  link_NAG-ASN         : angle       1.84933 (    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
  83 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8566 (m-30) cc_final: 0.8195 (m-30)
REVERT: C  424 LYS cc_start: 0.9014 (tptt) cc_final: 0.8696 (tppp)
REVERT: C  444 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8176 (mtmm)
REVERT: C  516 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6765 (tm-30)
REVERT: H   34 MET cc_start: 0.8547 (mmm) cc_final: 0.8246 (mmm)
REVERT: H   50 ASN cc_start: 0.7912 (t0) cc_final: 0.7683 (t0)
REVERT: H   60 ASN cc_start: 0.9066 (t0) cc_final: 0.8824 (t0)
REVERT: H   74 SER cc_start: 0.9191 (m) cc_final: 0.8959 (t)
REVERT: H   86 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6822 (mtp180)
REVERT: H   88 GLU cc_start: 0.9090 (pp20) cc_final: 0.8616 (pp20)
REVERT: H   89 ASP cc_start: 0.8161 (m-30) cc_final: 0.7925 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5733
  time to fit residues: 44.9749
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  : 0.059 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0170
   chunk 19 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
C 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.087443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.074965 restraints weight = 5995.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.23
r_work: 0.3083 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2556  Z= 0.146
  Angle     :  0.636   8.915   3482  Z= 0.308
  Chirality :  0.044   0.136    370
  Planarity :  0.004   0.041    448
  Dihedral  :  4.785  40.568    373
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 25.09 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.93 (0.45), residues: 310
  helix: -2.93 (1.16), residues: 20
  sheet:  0.02 (0.54), residues: 83
  loop : -0.63 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 403 
 TYR   0.014   0.001   TYR H  32 
 PHE   0.006   0.001   PHE C 347 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 2550)
  covalent geometry    : angle       0.63454 ( 3469)
  SS BOND              : bond        0.00206 (    5)
  SS BOND              : angle       0.45936 (   10)
  hydrogen bonds       : bond        0.02499 (   74)
  hydrogen bonds       : angle       6.30552 (  186)
  link_NAG-ASN         : bond        0.00225 (    1)
  link_NAG-ASN         : angle       1.86665 (    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
  82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8492 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8574 (m-30) cc_final: 0.8198 (m-30)
REVERT: C  424 LYS cc_start: 0.8993 (tptt) cc_final: 0.8738 (tppp)
REVERT: C  444 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8146 (mtmm)
REVERT: C  516 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6799 (tm-30)
REVERT: H   60 ASN cc_start: 0.9068 (t0) cc_final: 0.8820 (t0)
REVERT: H   74 SER cc_start: 0.9179 (m) cc_final: 0.8939 (t)
REVERT: H   86 ARG cc_start: 0.7479 (mtp180) cc_final: 0.6823 (mtp180)
REVERT: H   88 GLU cc_start: 0.9089 (pp20) cc_final: 0.8592 (pp20)
REVERT: H   89 ASP cc_start: 0.8177 (m-30) cc_final: 0.7919 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 77
  average time/residue: 0.5963
  time to fit residues: 46.7797
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  : 0.098 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0020
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.8392

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3409 r_free = 0.3409 target = 0.086386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.074060 restraints weight = 6039.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 3.21
r_work: 0.3067 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4138

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= 0.169
  Angle     :  0.676   9.838   3482  Z= 0.325
  Chirality :  0.046   0.138    370
  Planarity :  0.005   0.037    448
  Dihedral  :  4.961  43.020    373
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 25.09 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.95 (0.45), residues: 310
  helix: -2.90 (1.19), residues: 20
  sheet: -0.02 (0.54), residues: 83
  loop : -0.64 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 403 
 TYR   0.015   0.001   TYR H  52 
 PHE   0.006   0.001   PHE C 347 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 2550)
  covalent geometry    : angle       0.67446 ( 3469)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.49399 (   10)
  hydrogen bonds       : bond        0.02649 (   74)
  hydrogen bonds       : angle       6.35469 (  186)
  link_NAG-ASN         : bond        0.00212 (    1)
  link_NAG-ASN         : angle       1.95247 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1312.43 seconds
wall clock time: 22 minutes 57.86 seconds (1377.86 seconds total)