Starting phenix.real_space_refine
on Mon Nov 17 12:59:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dly_27520/11_2025/8dly_27520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dly_27520/11_2025/8dly_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_27520/11_2025/8dly_27520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dly_27520/11_2025/8dly_27520.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dly_27520/11_2025/8dly_27520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dly_27520/11_2025/8dly_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-2.0-5881/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: 0.84, per 1000 atoms: 0.34
  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 96.6 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: 0.10
  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: 0.37

  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:             4.150
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.060
  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:7.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.260
-------------------------------------------------------------------------------
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  : 0.105 
Fit side-chains
REVERT: C  420 ASP cc_start: 0.8522 (m-30) cc_final: 0.8206 (m-30)
REVERT: C  424 LYS cc_start: 0.8840 (tptt) cc_final: 0.8594 (tppp)
REVERT: C  456 PHE cc_start: 0.8663 (t80) cc_final: 0.8215 (t80)
REVERT: C  474 GLN cc_start: 0.7637 (mt0) cc_final: 0.7418 (mt0)
REVERT: H   39 GLN cc_start: 0.7728 (pt0) cc_final: 0.7151 (pm20)
REVERT: H   86 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6621 (mtp180)
REVERT: H   92 ILE cc_start: 0.8541 (mt) cc_final: 0.7759 (mm)
  outliers start: 1
  outliers final: 2
  residues processed: 100
  average time/residue: 0.5924
  time to fit residues: 60.4470
Evaluate side-chains
  63 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
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:    0.7980
   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:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.087260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075015 restraints weight = 6023.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.21
r_work: 0.3067 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2556  Z= 0.177
  Angle     :  0.623   6.527   3482  Z= 0.311
  Chirality :  0.044   0.147    370
  Planarity :  0.005   0.031    448
  Dihedral  :  8.947 126.776    377
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.48 %
    Favored  : 79.40 %
  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: -1.09 (0.42), residues: 310
  helix: -3.45 (0.78), residues: 27
  sheet:  0.05 (0.48), residues: 98
  loop : -0.68 (0.39), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  16 
 TYR   0.014   0.001   TYR H  79 
 PHE   0.008   0.001   PHE C 347 
 TRP   0.012   0.001   TRP H  47 
 HIS   0.004   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 2550)
  covalent geometry    : angle       0.62017 ( 3469)
  SS BOND              : bond        0.00469 (    5)
  SS BOND              : angle       0.64615 (   10)
  hydrogen bonds       : bond        0.03401 (   74)
  hydrogen bonds       : angle       7.31069 (  186)
  link_NAG-ASN         : bond        0.00339 (    1)
  link_NAG-ASN         : angle       2.07793 (    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
  82 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8711 (m-30) cc_final: 0.8459 (m-30)
REVERT: C  424 LYS cc_start: 0.8990 (tptt) cc_final: 0.8720 (tppp)
REVERT: H   29 PHE cc_start: 0.8609 (t80) cc_final: 0.8187 (t80)
REVERT: H   60 ASN cc_start: 0.9065 (t0) cc_final: 0.8859 (t0)
REVERT: H   86 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6665 (mtp180)
  outliers start: 11
  outliers final: 6
  residues processed: 78
  average time/residue: 0.5910
  time to fit residues: 47.0089
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  : 0.099 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.085609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.073470 restraints weight = 6092.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 3.15
r_work: 0.3043 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2556  Z= 0.144
  Angle     :  0.580   6.405   3482  Z= 0.293
  Chirality :  0.044   0.138    370
  Planarity :  0.004   0.032    448
  Dihedral  :  5.400  45.633    375
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 18.35 %
    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: -1.07 (0.43), residues: 310
  helix: -3.40 (1.09), residues: 20
  sheet: -0.03 (0.47), residues: 103
  loop : -0.76 (0.40), 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   0.012   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2550)
  covalent geometry    : angle       0.57641 ( 3469)
  SS BOND              : bond        0.00207 (    5)
  SS BOND              : angle       0.58439 (   10)
  hydrogen bonds       : bond        0.02944 (   74)
  hydrogen bonds       : angle       6.93938 (  186)
  link_NAG-ASN         : bond        0.00328 (    1)
  link_NAG-ASN         : angle       2.14184 (    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  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8683 (m-30) cc_final: 0.8422 (m-30)
REVERT: C  424 LYS cc_start: 0.9083 (tptt) cc_final: 0.8839 (tppp)
REVERT: C  444 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8147 (mtmm)
REVERT: H   60 ASN cc_start: 0.8989 (t0) cc_final: 0.8773 (t0)
REVERT: H   86 ARG cc_start: 0.7408 (mtp180) cc_final: 0.6734 (mtp180)
REVERT: H   88 GLU cc_start: 0.9036 (pp20) cc_final: 0.8687 (pp20)
REVERT: H   89 ASP cc_start: 0.8087 (m-30) cc_final: 0.7831 (m-30)
  outliers start: 15
  outliers final: 5
  residues processed: 81
  average time/residue: 0.4883
  time to fit residues: 40.4074
Evaluate side-chains
  71 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.085656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.073263 restraints weight = 5976.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 3.27
r_work: 0.3044 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3507

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= 0.180
  Angle     :  0.608   7.370   3482  Z= 0.301
  Chirality :  0.044   0.136    370
  Planarity :  0.004   0.032    448
  Dihedral  :  5.395  46.787    373
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 19.85 %
    Favored  : 73.78 %
  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 (0.44), residues: 310
  helix: -3.21 (1.18), residues: 20
  sheet: -0.11 (0.46), residues: 110
  loop : -0.72 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 403 
 TYR   0.011   0.001   TYR H  79 
 PHE   0.008   0.001   PHE C 347 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 2550)
  covalent geometry    : angle       0.60568 ( 3469)
  SS BOND              : bond        0.00254 (    5)
  SS BOND              : angle       0.44727 (   10)
  hydrogen bonds       : bond        0.02816 (   74)
  hydrogen bonds       : angle       6.81863 (  186)
  link_NAG-ASN         : bond        0.00268 (    1)
  link_NAG-ASN         : angle       2.10990 (    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: 17
    poor density    : 66
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8631 (m-30) cc_final: 0.8364 (m-30)
REVERT: C  424 LYS cc_start: 0.8995 (tptt) cc_final: 0.8654 (tppp)
REVERT: C  444 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8134 (mtmm)
REVERT: H   29 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7845 (t80)
REVERT: H   60 ASN cc_start: 0.9006 (t0) cc_final: 0.8802 (t0)
REVERT: H   74 SER cc_start: 0.9274 (m) cc_final: 0.9006 (t)
REVERT: H   86 ARG cc_start: 0.7389 (mtp180) cc_final: 0.6702 (mtp180)
REVERT: H   88 GLU cc_start: 0.9061 (pp20) cc_final: 0.8665 (pp20)
REVERT: H   89 ASP cc_start: 0.8220 (m-30) cc_final: 0.7861 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 76
  average time/residue: 0.4916
  time to fit residues: 38.1796
Evaluate side-chains
  78 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
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
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:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3385 r_free = 0.3385 target = 0.084790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.072642 restraints weight = 5888.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.17
r_work: 0.3035 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2556  Z= 0.180
  Angle     :  0.618   6.993   3482  Z= 0.304
  Chirality :  0.044   0.135    370
  Planarity :  0.004   0.035    448
  Dihedral  :  5.328  46.148    373
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 20.97 %
    Favored  : 73.03 %
  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: -1.18 (0.44), residues: 310
  helix: -3.05 (0.98), residues: 26
  sheet: -0.22 (0.46), residues: 104
  loop : -0.71 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 403 
 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   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 2550)
  covalent geometry    : angle       0.61483 ( 3469)
  SS BOND              : bond        0.00279 (    5)
  SS BOND              : angle       0.61548 (   10)
  hydrogen bonds       : bond        0.02739 (   74)
  hydrogen bonds       : angle       6.68087 (  186)
  link_NAG-ASN         : bond        0.00223 (    1)
  link_NAG-ASN         : angle       2.10482 (    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
  86 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8699 (ttm-80)
REVERT: C  420 ASP cc_start: 0.8624 (m-30) cc_final: 0.8350 (m-30)
REVERT: C  424 LYS cc_start: 0.8996 (tptt) cc_final: 0.8675 (tppp)
REVERT: C  444 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8151 (mtmm)
REVERT: H   29 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7408 (t80)
REVERT: H   39 GLN cc_start: 0.8086 (pt0) cc_final: 0.7693 (tt0)
REVERT: H   74 SER cc_start: 0.9269 (m) cc_final: 0.9000 (t)
REVERT: H   86 ARG cc_start: 0.7360 (mtp180) cc_final: 0.6706 (mtp180)
REVERT: H   88 GLU cc_start: 0.9060 (pp20) cc_final: 0.8625 (pp20)
  outliers start: 16
  outliers final: 9
  residues processed: 79
  average time/residue: 0.5040
  time to fit residues: 40.7543
Evaluate side-chains
  75 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  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   29 PHE
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:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0010
   chunk 17 optimal weight:    0.1980
   chunk 8 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.3384

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.087476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.075052 restraints weight = 5867.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.23
r_work: 0.3089 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2556  Z= 0.109
  Angle     :  0.589   8.909   3482  Z= 0.287
  Chirality :  0.043   0.132    370
  Planarity :  0.004   0.030    448
  Dihedral  :  4.801  39.325    373
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.85 %
    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: -0.98 (0.44), residues: 310
  helix: -3.14 (1.13), residues: 20
  sheet: -0.19 (0.47), residues: 104
  loop : -0.57 (0.42), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  16 
 TYR   0.014   0.001   TYR H 101 
 PHE   0.004   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
  covalent geometry    : bond        0.00257 ( 2550)
  covalent geometry    : angle       0.58728 ( 3469)
  SS BOND              : bond        0.00183 (    5)
  SS BOND              : angle       0.43452 (   10)
  hydrogen bonds       : bond        0.02382 (   74)
  hydrogen bonds       : angle       6.55092 (  186)
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       1.80215 (    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
  93 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8855 (ttp80) cc_final: 0.8505 (ttp80)
REVERT: C  408 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8454 (ptm-80)
REVERT: C  424 LYS cc_start: 0.8987 (tptt) cc_final: 0.8660 (tppp)
REVERT: C  444 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8129 (mtmm)
REVERT: C  517 LEU cc_start: 0.7328 (tt) cc_final: 0.7008 (tm)
REVERT: C  523 THR cc_start: 0.8543 (p) cc_final: 0.8228 (t)
REVERT: H   39 GLN cc_start: 0.8022 (pt0) cc_final: 0.7597 (tt0)
REVERT: H   50 ASN cc_start: 0.7888 (t0) cc_final: 0.7627 (t0)
REVERT: H   74 SER cc_start: 0.9244 (m) cc_final: 0.8990 (t)
REVERT: H   86 ARG cc_start: 0.7300 (mtp180) cc_final: 0.6716 (mtp180)
REVERT: H   88 GLU cc_start: 0.9097 (pp20) cc_final: 0.8587 (pp20)
REVERT: H   89 ASP cc_start: 0.8009 (m-30) cc_final: 0.7776 (m-30)
  outliers start: 13
  outliers final: 6
  residues processed: 86
  average time/residue: 0.5148
  time to fit residues: 45.2729
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0670
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6520

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.086894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.074626 restraints weight = 5901.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.21
r_work: 0.3069 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3932

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= 0.142
  Angle     :  0.629   8.798   3482  Z= 0.301
  Chirality :  0.044   0.135    370
  Planarity :  0.004   0.037    448
  Dihedral  :  4.865  40.510    373
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 24.34 %
    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: -1.03 (0.44), residues: 310
  helix: -3.06 (1.16), residues: 20
  sheet: -0.14 (0.51), residues: 90
  loop : -0.66 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   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 H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 2550)
  covalent geometry    : angle       0.62756 ( 3469)
  SS BOND              : bond        0.00234 (    5)
  SS BOND              : angle       0.45802 (   10)
  hydrogen bonds       : bond        0.02530 (   74)
  hydrogen bonds       : angle       6.42794 (  186)
  link_NAG-ASN         : bond        0.00252 (    1)
  link_NAG-ASN         : angle       1.84876 (    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
  87 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: C  403 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8485 (ttp80)
REVERT: C  424 LYS cc_start: 0.8993 (tptt) cc_final: 0.8631 (tppp)
REVERT: C  444 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8174 (mtmm)
REVERT: C  517 LEU cc_start: 0.7371 (tt) cc_final: 0.7025 (tm)
REVERT: C  523 THR cc_start: 0.8548 (p) cc_final: 0.8276 (t)
REVERT: H   39 GLN cc_start: 0.8074 (pt0) cc_final: 0.7640 (tt0)
REVERT: H   50 ASN cc_start: 0.7904 (t0) cc_final: 0.7645 (t0)
REVERT: H   74 SER cc_start: 0.9253 (m) cc_final: 0.9000 (t)
REVERT: H   86 ARG cc_start: 0.7330 (mtp180) cc_final: 0.6702 (mtp180)
REVERT: H   88 GLU cc_start: 0.9072 (pp20) cc_final: 0.8578 (pp20)
REVERT: H   89 ASP cc_start: 0.8122 (m-30) cc_final: 0.7902 (m-30)
REVERT: H   97 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6967 (ttt180)
  outliers start: 13
  outliers final: 8
  residues processed: 80
  average time/residue: 0.5803
  time to fit residues: 47.4470
Evaluate side-chains
  79 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
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 H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   78 LEU
Chi-restraints excluded: chain H residue   97 ARG
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:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0010
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.3384

-------------------------------------------------------------------------------
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 = 0.3452 r_free = 0.3452 target = 0.088427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.076093 restraints weight = 5958.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 3.21
r_work: 0.3107 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4011

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= 0.111
  Angle     :  0.610   8.232   3482  Z= 0.291
  Chirality :  0.044   0.132    370
  Planarity :  0.004   0.034    448
  Dihedral  :  4.532  35.715    373
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  5.24 %
    Allowed  : 25.09 %
    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: -0.96 (0.44), residues: 310
  helix: -3.02 (1.13), residues: 20
  sheet: -0.19 (0.50), residues: 92
  loop : -0.56 (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 H  52 
 PHE   0.004   0.001   PHE C 377 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 2550)
  covalent geometry    : angle       0.60928 ( 3469)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       0.36707 (   10)
  hydrogen bonds       : bond        0.02333 (   74)
  hydrogen bonds       : angle       6.24953 (  186)
  link_NAG-ASN         : bond        0.00278 (    1)
  link_NAG-ASN         : angle       1.66474 (    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
  94 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8412 (ptm-80)
REVERT: C  420 ASP cc_start: 0.8510 (m-30) cc_final: 0.8148 (m-30)
REVERT: C  424 LYS cc_start: 0.8971 (tptt) cc_final: 0.8605 (tppp)
REVERT: C  444 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8164 (mtmm)
REVERT: C  517 LEU cc_start: 0.7376 (tt) cc_final: 0.7018 (tm)
REVERT: C  523 THR cc_start: 0.8487 (p) cc_final: 0.8209 (t)
REVERT: H   39 GLN cc_start: 0.8042 (pt0) cc_final: 0.7662 (tt0)
REVERT: H   74 SER cc_start: 0.9205 (m) cc_final: 0.8958 (t)
REVERT: H   86 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6695 (mtp180)
REVERT: H   88 GLU cc_start: 0.9106 (pp20) cc_final: 0.8625 (pp20)
REVERT: H   97 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6934 (ttt180)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.5404
  time to fit residues: 48.0327
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  : 0.099 
-------------------------------------------------------------------------------
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 H residue    2 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   97 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.086287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.074119 restraints weight = 6027.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 3.15
r_work: 0.3082 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   2556  Z= 0.151
  Angle     :  0.644   8.554   3482  Z= 0.313
  Chirality :  0.044   0.134    370
  Planarity :  0.004   0.037    448
  Dihedral  :  4.720  38.979    373
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 25.09 %
    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: -0.96 (0.44), residues: 310
  helix: -2.88 (1.18), residues: 20
  sheet: -0.05 (0.53), 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   0.013   0.001   TYR H  52 
 PHE   0.022   0.001   PHE H  27 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 2550)
  covalent geometry    : angle       0.64282 ( 3469)
  SS BOND              : bond        0.00287 (    5)
  SS BOND              : angle       0.38964 (   10)
  hydrogen bonds       : bond        0.02567 (   74)
  hydrogen bonds       : angle       6.28337 (  186)
  link_NAG-ASN         : bond        0.00215 (    1)
  link_NAG-ASN         : angle       1.77711 (    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
  85 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8545 (m-30) cc_final: 0.8166 (m-30)
REVERT: C  424 LYS cc_start: 0.8975 (tptt) cc_final: 0.8613 (tppp)
REVERT: C  444 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8190 (mtmm)
REVERT: C  517 LEU cc_start: 0.7038 (tt) cc_final: 0.6666 (tm)
REVERT: C  523 THR cc_start: 0.8515 (p) cc_final: 0.8260 (t)
REVERT: H   39 GLN cc_start: 0.8056 (pt0) cc_final: 0.7683 (tt0)
REVERT: H   74 SER cc_start: 0.9206 (m) cc_final: 0.8958 (t)
REVERT: H   86 ARG cc_start: 0.7430 (mtp180) cc_final: 0.6766 (mtp180)
REVERT: H   88 GLU cc_start: 0.9065 (pp20) cc_final: 0.8561 (pp20)
REVERT: H   89 ASP cc_start: 0.8167 (m-30) cc_final: 0.7917 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 78
  average time/residue: 0.5922
  time to fit residues: 47.1241
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  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  368 LEU
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 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:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.1980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.087533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.075279 restraints weight = 6011.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 3.15
r_work: 0.3099 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4118

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= 0.134
  Angle     :  0.643   9.757   3482  Z= 0.310
  Chirality :  0.044   0.134    370
  Planarity :  0.004   0.037    448
  Dihedral  :  4.635  38.208    373
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 26.59 %
    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: -0.97 (0.45), residues: 310
  helix: -2.93 (1.17), residues: 20
  sheet: -0.06 (0.53), residues: 83
  loop : -0.63 (0.41), 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  32 
 PHE   0.005   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        0.00319 ( 2550)
  covalent geometry    : angle       0.64207 ( 3469)
  SS BOND              : bond        0.00205 (    5)
  SS BOND              : angle       0.35134 (   10)
  hydrogen bonds       : bond        0.02501 (   74)
  hydrogen bonds       : angle       6.33736 (  186)
  link_NAG-ASN         : bond        0.00242 (    1)
  link_NAG-ASN         : angle       1.77371 (    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
  84 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: C  420 ASP cc_start: 0.8508 (m-30) cc_final: 0.8137 (m-30)
REVERT: C  424 LYS cc_start: 0.8932 (tptt) cc_final: 0.8659 (tppp)
REVERT: C  444 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8148 (mtmm)
REVERT: C  517 LEU cc_start: 0.7040 (tt) cc_final: 0.6655 (tm)
REVERT: C  523 THR cc_start: 0.8502 (p) cc_final: 0.8244 (t)
REVERT: H   39 GLN cc_start: 0.8070 (pt0) cc_final: 0.7695 (tt0)
REVERT: H   74 SER cc_start: 0.9210 (m) cc_final: 0.8973 (t)
REVERT: H   86 ARG cc_start: 0.7396 (mtp180) cc_final: 0.6738 (mtp180)
REVERT: H   88 GLU cc_start: 0.9098 (pp20) cc_final: 0.8570 (pp20)
REVERT: H   89 ASP cc_start: 0.8193 (m-30) cc_final: 0.7941 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 78
  average time/residue: 0.5436
  time to fit residues: 43.2494
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  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  368 LEU
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3425 r_free = 0.3425 target = 0.086811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.074664 restraints weight = 6005.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 3.12
r_work: 0.3087 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4210

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= 0.149
  Angle     :  0.671   9.154   3482  Z= 0.322
  Chirality :  0.045   0.180    370
  Planarity :  0.005   0.051    448
  Dihedral  :  4.699  38.899    373
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 27.72 %
    Favored  : 68.54 %
  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: -0.97 (0.45), residues: 310
  helix: -2.91 (1.18), residues: 20
  sheet: -0.06 (0.53), residues: 83
  loop : -0.64 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 403 
 TYR   0.012   0.001   TYR H  32 
 PHE   0.007   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2550)
  covalent geometry    : angle       0.66957 ( 3469)
  SS BOND              : bond        0.00260 (    5)
  SS BOND              : angle       0.39504 (   10)
  hydrogen bonds       : bond        0.02557 (   74)
  hydrogen bonds       : angle       6.33707 (  186)
  link_NAG-ASN         : bond        0.00224 (    1)
  link_NAG-ASN         : angle       1.83702 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1325.60 seconds
wall clock time: 23 minutes 19.23 seconds (1399.23 seconds total)