Starting phenix.real_space_refine
on Tue Mar  3 11:37:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zcf_14629/03_2026/7zcf_14629.cif"
  }
  resolution = 4.0
  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=  -0.004 sd=   0.044
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      14      5.16       5
     C    2107      2.51       5
     N     556      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  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: 3312
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "E"
      Number of atoms: 1703
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1703
          Classifications: {'peptide': 225}
          Link IDs: {'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
    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: 0.80, per 1000 atoms: 0.24
  Number of scatterers: 3312
  At special positions: 0
  Unit cell: (65.786, 91.567, 90.678, 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      14     16.00
     O     635      8.00
     N     556      7.00
     C    2107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, 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=2.04
    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=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " 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: 0.24
  Conformation dependent library (CDL) restraints added in 105.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 6 sheets defined
      8.5% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.854A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
      removed outlier: 4.228A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ASN C 370 " --> pdb=" O   SER C 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 365 through 370'
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.676A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.585A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN C 409 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 443
      removed outlier: 3.877A  pdb=" N   SER C 443 " --> pdb=" O   ASN C 440 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.954A  pdb=" N   PHE E 217 " --> pdb=" O   PRO E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.651A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
      removed outlier: 3.640A  pdb=" N   GLN C 493 " --> pdb=" O   TYR C 453 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20
      removed outlier: 3.639A  pdb=" N   LEU E  80 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   THR E  68 " --> pdb=" O   GLN E  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59
      removed outlier: 5.179A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   TYR E  33 " --> pdb=" O   ASP E  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188
      removed outlier: 3.778A  pdb=" N   SER E 187 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.234A  pdb=" N   LEU E 167 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR E 231 " --> pdb=" O   GLN E 224 " (cutoff:3.500A)

    54 hydrogen bonds defined for protein.
    132 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: 0.49

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1057
        1.35 -     1.46: 899
        1.46 -     1.58: 1423
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3395
  Sorted by residual:
  bond pdb=" C   PRO E 174 "
       pdb=" O   PRO E 174 "
    ideal  model  delta    sigma   weight residual
    1.235  1.268 -0.033 1.30e-02 5.92e+03 6.36e+00
  bond pdb=" C   PRO E 174 "
       pdb=" N   GLY E 175 "
    ideal  model  delta    sigma   weight residual
    1.333  1.368 -0.036 1.57e-02 4.06e+03 5.19e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C   SER E 228 "
       pdb=" N   PRO E 229 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.64e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 3390 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 4379
        1.33 -     2.66: 180
        2.66 -     4.00: 46
        4.00 -     5.33: 7
        5.33 -     6.66: 2
  Bond angle restraints: 4614
  Sorted by residual:
  angle pdb=" N   SER E 140 "
        pdb=" CA  SER E 140 "
        pdb=" C   SER E 140 "
      ideal   model   delta    sigma   weight residual
     109.81  116.47   -6.66 2.21e+00 2.05e-01 9.08e+00
  angle pdb=" N   GLY C 526 "
        pdb=" CA  GLY C 526 "
        pdb=" C   GLY C 526 "
      ideal   model   delta    sigma   weight residual
     112.34  118.46   -6.12 2.04e+00 2.40e-01 8.99e+00
  angle pdb=" N   GLN E 110 "
        pdb=" CA  GLN E 110 "
        pdb=" C   GLN E 110 "
      ideal   model   delta    sigma   weight residual
     114.04  110.83    3.21 1.24e+00 6.50e-01 6.71e+00
  angle pdb=" O   PRO E 174 "
        pdb=" C   PRO E 174 "
        pdb=" N   GLY E 175 "
      ideal   model   delta    sigma   weight residual
     122.64  126.13   -3.49 1.35e+00 5.49e-01 6.68e+00
  angle pdb=" N   PRO C 337 "
        pdb=" CA  PRO C 337 "
        pdb=" C   PRO C 337 "
      ideal   model   delta    sigma   weight residual
     114.68  112.10    2.58 1.04e+00 9.25e-01 6.13e+00
  ... (remaining 4609 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1812
       17.95 -    35.91: 160
       35.91 -    53.86: 35
       53.86 -    71.82: 4
       71.82 -    89.77: 4
  Dihedral angle restraints: 2015
    sinusoidal: 790
      harmonic: 1225
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.90   45.10     1      1.00e+01 1.00e-02 2.82e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.62  -44.62     1      1.00e+01 1.00e-02 2.77e+01
  dihedral pdb=" CA  SER E 140 "
           pdb=" C   SER E 140 "
           pdb=" N   PRO E 141 "
           pdb=" CA  PRO E 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.22  -23.78     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 2012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 398
       0.049 -    0.097: 80
       0.097 -    0.146: 19
       0.146 -    0.194: 2
       0.194 -    0.243: 1
  Chirality restraints: 500
  Sorted by residual:
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE C 472 "
            pdb=" N   ILE C 472 "
            pdb=" C   ILE C 472 "
            pdb=" CB  ILE C 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.30e-01
  chirality pdb=" CB  VAL E 116 "
            pdb=" CA  VAL E 116 "
            pdb=" CG1 VAL E 116 "
            pdb=" CG2 VAL E 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 497 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.035 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO C 337 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 506 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 507 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 507 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 507 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 411 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO C 412 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 412 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 412 "    0.018 5.00e-02 4.00e+02
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 42
        2.65 -     3.21: 2931
        3.21 -     3.78: 4503
        3.78 -     4.34: 6072
        4.34 -     4.90: 10024
  Nonbonded interactions: 23572
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 354 "
            pdb=" OG  SER C 399 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   LEU C 455 "
            pdb=" OH  TYR E  33 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OD1 ASN C 331 "
            pdb=" N   ILE C 332 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OH  TYR C 421 "
            pdb=" O   PRO E  53 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" N   GLN E   3 "
            pdb=" OG  SER E  25 "
     model   vdw
     2.311 3.120
  ... (remaining 23567 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.750
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.780
  Find NCS groups from input model:        0.020
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3402  Z= 0.143
  Angle     :  0.660   6.658   4629  Z= 0.371
  Chirality :  0.045   0.243    500
  Planarity :  0.005   0.054    597
  Dihedral  : 14.299  89.770   1223
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  0.28 %
    Favored  : 99.16 %
  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: -2.45 (0.40), residues: 420
  helix: -4.94 (0.47), residues: 8
  sheet: -0.46 (0.55), residues: 104
  loop : -2.12 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  71 
 TYR   0.012   0.001   TYR C 473 
 PHE   0.015   0.001   PHE C 338 
 TRP   0.007   0.001   TRP C 353 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3395)
  covalent geometry    : angle       0.65843 ( 4614)
  SS BOND              : bond        0.00217 (    6)
  SS BOND              : angle       0.93469 (   12)
  hydrogen bonds       : bond        0.18437 (   54)
  hydrogen bonds       : angle       6.93570 (  132)
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       1.22629 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 71
  average time/residue: 0.0718
  time to fit residues: 6.2400
Evaluate side-chains
  58 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  139 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0270
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.168985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.149825 restraints weight = 5756.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.152899 restraints weight = 3635.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.155052 restraints weight = 2615.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.156564 restraints weight = 2043.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.157723 restraints weight = 1704.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3402  Z= 0.153
  Angle     :  0.662   7.071   4629  Z= 0.346
  Chirality :  0.046   0.176    500
  Planarity :  0.005   0.038    597
  Dihedral  :  6.328  50.973    496
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.57 %
    Favored  : 86.03 %
  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: -2.58 (0.41), residues: 420
  helix: -4.88 (0.50), residues: 8
  sheet: -1.27 (0.49), residues: 121
  loop : -1.92 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  71 
 TYR   0.025   0.002   TYR E 183 
 PHE   0.013   0.002   PHE C 342 
 TRP   0.010   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3395)
  covalent geometry    : angle       0.65724 ( 4614)
  SS BOND              : bond        0.00570 (    6)
  SS BOND              : angle       1.71204 (   12)
  hydrogen bonds       : bond        0.03815 (   54)
  hydrogen bonds       : angle       6.04330 (  132)
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       1.06290 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0520
  time to fit residues: 5.1326
Evaluate side-chains
  67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0020
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.163837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.144788 restraints weight = 5846.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147800 restraints weight = 3684.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.149913 restraints weight = 2634.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.151195 restraints weight = 2052.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.152321 restraints weight = 1729.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3716 r_free = 0.3716    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3402  Z= 0.184
  Angle     :  0.717   7.274   4629  Z= 0.379
  Chirality :  0.047   0.170    500
  Planarity :  0.005   0.037    597
  Dihedral  :  6.655  52.293    493
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.10 %
    Favored  : 81.90 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.76 %
    Favored  : 79.33 %
  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: -2.72 (0.41), residues: 420
  helix: -4.86 (0.52), residues: 8
  sheet: -1.43 (0.48), residues: 128
  loop : -1.99 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  97 
 TYR   0.025   0.002   TYR E 183 
 PHE   0.015   0.002   PHE C 342 
 TRP   0.016   0.002   TRP C 353 
 HIS   0.003   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 3395)
  covalent geometry    : angle       0.71259 ( 4614)
  SS BOND              : bond        0.00728 (    6)
  SS BOND              : angle       1.68015 (   12)
  hydrogen bonds       : bond        0.04142 (   54)
  hydrogen bonds       : angle       6.40111 (  132)
  link_NAG-ASN         : bond        0.00133 (    1)
  link_NAG-ASN         : angle       0.91177 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.078 
Fit side-chains
REVERT: C  331 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6866 (p0)
REVERT: C  353 TRP cc_start: 0.8729 (p-90) cc_final: 0.8258 (p-90)
REVERT: C  401 VAL cc_start: 0.9444 (OUTLIER) cc_final: 0.9228 (p)
REVERT: C  450 ASN cc_start: 0.8813 (p0) cc_final: 0.8206 (p0)
REVERT: E  139 GLN cc_start: 0.7118 (pt0) cc_final: 0.6599 (pt0)
  outliers start: 14
  outliers final: 8
  residues processed: 66
  average time/residue: 0.0623
  time to fit residues: 5.0779
Evaluate side-chains
  69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  331 ASN
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  518 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.143213 restraints weight = 5785.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.146229 restraints weight = 3643.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.148274 restraints weight = 2602.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.149751 restraints weight = 2027.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.150594 restraints weight = 1690.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3402  Z= 0.160
  Angle     :  0.697   6.999   4629  Z= 0.364
  Chirality :  0.045   0.181    500
  Planarity :  0.005   0.031    597
  Dihedral  :  6.543  50.406    493
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.38 %
    Favored  : 82.62 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 18.16 %
    Favored  : 77.65 %
  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: -2.77 (0.41), residues: 420
  helix: -4.72 (0.64), residues: 8
  sheet: -1.47 (0.49), residues: 123
  loop : -2.03 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  97 
 TYR   0.023   0.002   TYR E 183 
 PHE   0.011   0.002   PHE C 342 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3395)
  covalent geometry    : angle       0.68906 ( 4614)
  SS BOND              : bond        0.00577 (    6)
  SS BOND              : angle       2.13403 (   12)
  hydrogen bonds       : bond        0.03614 (   54)
  hydrogen bonds       : angle       6.08930 (  132)
  link_NAG-ASN         : bond        0.00185 (    1)
  link_NAG-ASN         : angle       0.93408 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: C  401 VAL cc_start: 0.9452 (OUTLIER) cc_final: 0.9237 (p)
REVERT: C  450 ASN cc_start: 0.8787 (p0) cc_final: 0.8193 (p0)
REVERT: E  139 GLN cc_start: 0.7231 (pt0) cc_final: 0.6696 (pt0)
REVERT: E  215 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7705 (tm-30)
REVERT: E  224 GLN cc_start: 0.8719 (pp30) cc_final: 0.8388 (pp30)
  outliers start: 15
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0560
  time to fit residues: 4.9219
Evaluate side-chains
  71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0030
   chunk 41 optimal weight:    0.0270
   chunk 30 optimal weight:    0.7980
   chunk 27 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.3448

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.163415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.144755 restraints weight = 5806.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.147738 restraints weight = 3657.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.149934 restraints weight = 2616.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.150990 restraints weight = 2031.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152245 restraints weight = 1734.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3402  Z= 0.127
  Angle     :  0.657   6.737   4629  Z= 0.340
  Chirality :  0.045   0.175    500
  Planarity :  0.004   0.031    597
  Dihedral  :  6.211  50.806    493
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.24 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.55 %
    Favored  : 77.09 %
  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: -2.78 (0.41), residues: 420
  helix: -4.77 (0.59), residues: 8
  sheet: -1.49 (0.49), residues: 124
  loop : -2.03 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  97 
 TYR   0.022   0.001   TYR E 183 
 PHE   0.010   0.001   PHE E  27 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3395)
  covalent geometry    : angle       0.65443 ( 4614)
  SS BOND              : bond        0.00525 (    6)
  SS BOND              : angle       1.21698 (   12)
  hydrogen bonds       : bond        0.03288 (   54)
  hydrogen bonds       : angle       5.94996 (  132)
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       0.81481 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8742 (p-90) cc_final: 0.8248 (p-90)
REVERT: C  450 ASN cc_start: 0.8752 (p0) cc_final: 0.8166 (p0)
REVERT: E  139 GLN cc_start: 0.7236 (pt0) cc_final: 0.6753 (pt0)
REVERT: E  215 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: E  224 GLN cc_start: 0.8668 (pp30) cc_final: 0.8392 (pp30)
  outliers start: 12
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0503
  time to fit residues: 4.5246
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.0040
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
** E  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.139711 restraints weight = 5845.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.142532 restraints weight = 3665.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.144546 restraints weight = 2625.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145695 restraints weight = 2057.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.146851 restraints weight = 1735.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3402  Z= 0.176
  Angle     :  0.710   7.299   4629  Z= 0.371
  Chirality :  0.048   0.293    500
  Planarity :  0.005   0.031    597
  Dihedral  :  6.590  50.545    493
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.81 %
    Favored  : 81.19 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 18.44 %
    Favored  : 75.98 %
  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: -2.97 (0.41), residues: 420
  helix: -4.69 (0.67), residues: 8
  sheet: -1.58 (0.49), residues: 123
  loop : -2.19 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  97 
 TYR   0.020   0.002   TYR E 183 
 PHE   0.010   0.002   PHE E 205 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 3395)
  covalent geometry    : angle       0.70303 ( 4614)
  SS BOND              : bond        0.00627 (    6)
  SS BOND              : angle       2.08715 (   12)
  hydrogen bonds       : bond        0.03713 (   54)
  hydrogen bonds       : angle       6.26074 (  132)
  link_NAG-ASN         : bond        0.00288 (    1)
  link_NAG-ASN         : angle       0.89072 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8847 (p-90) cc_final: 0.8296 (p-90)
REVERT: C  450 ASN cc_start: 0.8806 (p0) cc_final: 0.8265 (p0)
REVERT: E  139 GLN cc_start: 0.7300 (pt0) cc_final: 0.6773 (pt0)
REVERT: E  215 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7434 (tm-30)
REVERT: E  224 GLN cc_start: 0.8671 (pp30) cc_final: 0.8346 (pp30)
  outliers start: 20
  outliers final: 16
  residues processed: 76
  average time/residue: 0.0588
  time to fit residues: 5.5487
Evaluate side-chains
  76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.159356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140986 restraints weight = 5860.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.143958 restraints weight = 3657.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.146030 restraints weight = 2590.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.147363 restraints weight = 2011.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148456 restraints weight = 1687.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.4389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3402  Z= 0.153
  Angle     :  0.693   7.117   4629  Z= 0.358
  Chirality :  0.047   0.263    500
  Planarity :  0.004   0.032    597
  Dihedral  :  6.373  50.390    493
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.71 %
    Favored  : 84.29 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 21.51 %
    Favored  : 74.02 %
  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: -2.90 (0.41), residues: 420
  helix: -4.57 (0.77), residues: 8
  sheet: -1.57 (0.50), residues: 122
  loop : -2.12 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  97 
 TYR   0.017   0.001   TYR C 473 
 PHE   0.011   0.001   PHE E  27 
 TRP   0.014   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3395)
  covalent geometry    : angle       0.68994 ( 4614)
  SS BOND              : bond        0.00560 (    6)
  SS BOND              : angle       1.33704 (   12)
  hydrogen bonds       : bond        0.03484 (   54)
  hydrogen bonds       : angle       6.24569 (  132)
  link_NAG-ASN         : bond        0.00361 (    1)
  link_NAG-ASN         : angle       0.89487 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8847 (p-90) cc_final: 0.8296 (p-90)
REVERT: C  450 ASN cc_start: 0.8809 (p0) cc_final: 0.8288 (p0)
REVERT: E  139 GLN cc_start: 0.7272 (pt0) cc_final: 0.6799 (pt0)
REVERT: E  215 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: E  224 GLN cc_start: 0.8674 (pp30) cc_final: 0.8335 (pp30)
  outliers start: 16
  outliers final: 15
  residues processed: 72
  average time/residue: 0.0614
  time to fit residues: 5.5823
Evaluate side-chains
  78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.0020
   chunk 37 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0270
   overall best weight:    0.3846

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.159614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.141309 restraints weight = 5931.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.144238 restraints weight = 3742.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.146272 restraints weight = 2679.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.147488 restraints weight = 2096.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.148772 restraints weight = 1768.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3402  Z= 0.135
  Angle     :  0.674   7.091   4629  Z= 0.348
  Chirality :  0.046   0.239    500
  Planarity :  0.004   0.033    597
  Dihedral  :  6.209  50.668    493
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.14 %
    Favored  : 82.86 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 20.67 %
    Favored  : 73.74 %
  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: -2.83 (0.41), residues: 420
  helix: -4.55 (0.79), residues: 8
  sheet: -1.54 (0.49), residues: 124
  loop : -2.07 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  97 
 TYR   0.018   0.001   TYR C 473 
 PHE   0.009   0.001   PHE E  27 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3395)
  covalent geometry    : angle       0.66482 ( 4614)
  SS BOND              : bond        0.00640 (    6)
  SS BOND              : angle       2.23623 (   12)
  hydrogen bonds       : bond        0.03289 (   54)
  hydrogen bonds       : angle       6.07317 (  132)
  link_NAG-ASN         : bond        0.00367 (    1)
  link_NAG-ASN         : angle       0.84274 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.8824 (p-90) cc_final: 0.8335 (p-90)
REVERT: C  450 ASN cc_start: 0.8738 (p0) cc_final: 0.8262 (p0)
REVERT: E   71 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7751 (ptm-80)
REVERT: E  215 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7371 (tm-30)
REVERT: E  224 GLN cc_start: 0.8667 (pp30) cc_final: 0.8350 (pp30)
  outliers start: 20
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0656
  time to fit residues: 5.9188
Evaluate side-chains
  81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue   71 ARG
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 3 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
E 139 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.156862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.138273 restraints weight = 5969.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.141190 restraints weight = 3754.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143276 restraints weight = 2679.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.144555 restraints weight = 2091.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.145650 restraints weight = 1764.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3402  Z= 0.179
  Angle     :  0.727   6.986   4629  Z= 0.377
  Chirality :  0.047   0.232    500
  Planarity :  0.005   0.033    597
  Dihedral  :  6.615  51.391    493
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.24 %
    Favored  : 79.76 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 20.11 %
    Favored  : 74.02 %
  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: -2.97 (0.41), residues: 420
  helix: -4.57 (0.77), residues: 8
  sheet: -1.71 (0.49), residues: 119
  loop : -2.14 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  97 
 TYR   0.017   0.002   TYR C 473 
 PHE   0.009   0.001   PHE E 205 
 TRP   0.015   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 3395)
  covalent geometry    : angle       0.71973 ( 4614)
  SS BOND              : bond        0.00667 (    6)
  SS BOND              : angle       2.16978 (   12)
  hydrogen bonds       : bond        0.03705 (   54)
  hydrogen bonds       : angle       6.38636 (  132)
  link_NAG-ASN         : bond        0.00400 (    1)
  link_NAG-ASN         : angle       1.04775 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.090 
Fit side-chains
REVERT: C  353 TRP cc_start: 0.8889 (p-90) cc_final: 0.8318 (p-90)
REVERT: C  450 ASN cc_start: 0.8857 (p0) cc_final: 0.8411 (p0)
REVERT: E   29 VAL cc_start: 0.9245 (m) cc_final: 0.8984 (m)
REVERT: E   71 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7796 (ptm-80)
REVERT: E  139 GLN cc_start: 0.7308 (pt0) cc_final: 0.6890 (pt0)
REVERT: E  215 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7358 (tm-30)
REVERT: E  224 GLN cc_start: 0.8711 (pp30) cc_final: 0.8328 (pp30)
  outliers start: 21
  outliers final: 18
  residues processed: 76
  average time/residue: 0.0667
  time to fit residues: 6.2120
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue   71 ARG
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0470
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0040
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.7292

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.155686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.137594 restraints weight = 5921.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.140478 restraints weight = 3721.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.142402 restraints weight = 2651.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143530 restraints weight = 2082.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.144747 restraints weight = 1769.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.4870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3402  Z= 0.191
  Angle     :  0.757   7.243   4629  Z= 0.396
  Chirality :  0.048   0.239    500
  Planarity :  0.005   0.033    597
  Dihedral  :  6.637  50.880    493
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.57 %
    Favored  : 81.43 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 21.23 %
    Favored  : 73.46 %
  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: -3.06 (0.41), residues: 420
  helix: -4.49 (0.84), residues: 8
  sheet: -1.78 (0.49), residues: 119
  loop : -2.20 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  97 
 TYR   0.016   0.002   TYR C 473 
 PHE   0.009   0.002   PHE E  27 
 TRP   0.014   0.001   TRP C 436 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 3395)
  covalent geometry    : angle       0.75407 ( 4614)
  SS BOND              : bond        0.00474 (    6)
  SS BOND              : angle       1.44340 (   12)
  hydrogen bonds       : bond        0.03853 (   54)
  hydrogen bonds       : angle       6.47298 (  132)
  link_NAG-ASN         : bond        0.00415 (    1)
  link_NAG-ASN         : angle       1.19629 (    3)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.126 
Fit side-chains
REVERT: C  450 ASN cc_start: 0.8867 (p0) cc_final: 0.8292 (p0)
REVERT: E   29 VAL cc_start: 0.9250 (m) cc_final: 0.9014 (m)
REVERT: E   71 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7822 (ptm-80)
REVERT: E  139 GLN cc_start: 0.7371 (pt0) cc_final: 0.6985 (pt0)
REVERT: E  215 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7527 (tm-30)
  outliers start: 19
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0646
  time to fit residues: 5.7487
Evaluate side-chains
  77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  338 PHE
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  473 TYR
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain E residue   35 SER
Chi-restraints excluded: chain E residue   46 GLU
Chi-restraints excluded: chain E residue   69 ILE
Chi-restraints excluded: chain E residue   71 ARG
Chi-restraints excluded: chain E residue  138 THR
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  182 ILE
Chi-restraints excluded: chain E residue  199 SER
Chi-restraints excluded: chain E residue  231 THR
Chi-restraints excluded: chain E residue  240 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0970
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   overall best weight:    0.3536

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.159485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.141694 restraints weight = 5894.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.144696 restraints weight = 3636.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.146819 restraints weight = 2556.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.148037 restraints weight = 1973.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.149181 restraints weight = 1652.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3402  Z= 0.138
  Angle     :  0.726   8.309   4629  Z= 0.373
  Chirality :  0.046   0.221    500
  Planarity :  0.005   0.032    597
  Dihedral  :  6.328  51.192    493
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.90 %
    Favored  : 83.10 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 22.35 %
    Favored  : 72.91 %
  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: -2.94 (0.41), residues: 420
  helix: -4.36 (0.97), residues: 8
  sheet: -1.62 (0.49), residues: 124
  loop : -2.15 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  97 
 TYR   0.017   0.001   TYR C 473 
 PHE   0.010   0.001   PHE E  27 
 TRP   0.015   0.001   TRP C 436 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3395)
  covalent geometry    : angle       0.71766 ( 4614)
  SS BOND              : bond        0.00795 (    6)
  SS BOND              : angle       2.21109 (   12)
  hydrogen bonds       : bond        0.03486 (   54)
  hydrogen bonds       : angle       6.28168 (  132)
  link_NAG-ASN         : bond        0.00459 (    1)
  link_NAG-ASN         : angle       0.85454 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 892.88 seconds
wall clock time: 15 minutes 59.74 seconds (959.74 seconds total)