Starting phenix.real_space_refine
on Wed Jul  1 22:09:14 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3s_35155/07_2026/8i3s_35155.cif"
  }
  resolution = 3.9
  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=  -0.003 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      16      5.16       5
     C    2074      2.51       5
     N     554      2.21       5
     O     628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3272
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 897
          Classifications: {'peptide': 118}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112}
    Chain: "L"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 809
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.71, per 1000 atoms: 0.22
  Number of scatterers: 3272
  At special positions: 0
  Unit cell: (67.45, 68.4, 96.9, 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      16     16.00
     O     628      8.00
     N     554      7.00
     C    2074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=1.56
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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 A1301 " - " ASN A 343 "
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 118.6 milliseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 9 sheets defined
      10.7% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 344
      removed outlier: 3.873A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.658A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
      removed outlier: 3.542A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 4.000A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.725A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG A 509 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.189A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7
      removed outlier: 3.679A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 13
      removed outlier: 7.060A  pdb=" N   LYS H  12 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 59
      removed outlier: 3.670A  pdb=" N   ARG H  56 " --> pdb=" O   ILE H  52 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE H  52 " --> pdb=" O   ARG H  56 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   TYR H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   ARG H  38 " --> pdb=" O   TYR H  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 24
    Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 46

    82 hydrogen bonds defined for protein.
    207 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: 0.44

  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:
        1.21 -     1.33: 863
        1.33 -     1.45: 679
        1.45 -     1.57: 1787
        1.57 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 3349
  Sorted by residual:
  bond pdb=" N   PRO L  59 "
       pdb=" CA  PRO L  59 "
    ideal  model  delta    sigma   weight residual
    1.468  1.440  0.027 7.90e-03 1.60e+04 1.21e+01
  bond pdb=" N   ASN H  32 "
       pdb=" CA  ASN H  32 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.19e-02 7.06e+03 1.02e+01
  bond pdb=" N   PHE L  62 "
       pdb=" CA  PHE L  62 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.21e-02 6.83e+03 6.49e+00
  bond pdb=" N   ILE L  58 "
       pdb=" CA  ILE L  58 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.23e-02 6.61e+03 5.41e+00
  bond pdb=" CA  SER L  63 "
       pdb=" CB  SER L  63 "
    ideal  model  delta    sigma   weight residual
    1.529  1.499  0.030 1.54e-02 4.22e+03 3.78e+00
  ... (remaining 3344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 4343
        1.17 -     2.34: 152
        2.34 -     3.51: 38
        3.51 -     4.68: 10
        4.68 -     5.85: 4
  Bond angle restraints: 4547
  Sorted by residual:
  angle pdb=" CA  ALA L  60 "
        pdb=" C   ALA L  60 "
        pdb=" O   ALA L  60 "
      ideal   model   delta    sigma   weight residual
     120.81  116.22    4.59 1.15e+00 7.56e-01 1.60e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     113.12  107.27    5.85 1.65e+00 3.67e-01 1.26e+01
  angle pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
        pdb=" O   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     121.38  118.69    2.69 7.70e-01 1.69e+00 1.22e+01
  angle pdb=" C   ILE H  31 "
        pdb=" N   ASN H  32 "
        pdb=" CA  ASN H  32 "
      ideal   model   delta    sigma   weight residual
     122.87  117.62    5.25 1.61e+00 3.86e-01 1.06e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CD  PRO L  59 "
        pdb=" CG  PRO L  59 "
      ideal   model   delta    sigma   weight residual
     103.20   98.41    4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 4542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.35: 1759
       12.35 -    24.70: 149
       24.70 -    37.05: 50
       37.05 -    49.40: 12
       49.40 -    61.75: 9
  Dihedral angle restraints: 1979
    sinusoidal: 768
      harmonic: 1211
  Sorted by residual:
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -114.61   28.61     1      1.00e+01 1.00e-02 1.17e+01
  dihedral pdb=" CA  ARG L  61 "
           pdb=" CB  ARG L  61 "
           pdb=" CG  ARG L  61 "
           pdb=" CD  ARG L  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  123.29   56.71     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" CA  ILE A 434 "
           pdb=" CB  ILE A 434 "
           pdb=" CG1 ILE A 434 "
           pdb=" CD1 ILE A 434 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.51  -55.51     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1976 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 387
       0.046 -    0.092: 74
       0.092 -    0.138: 31
       0.138 -    0.184: 4
       0.184 -    0.230: 1
  Chirality restraints: 497
  Sorted by residual:
  chirality pdb=" CA  PHE L  62 "
            pdb=" N   PHE L  62 "
            pdb=" C   PHE L  62 "
            pdb=" CB  PHE L  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  ALA L  60 "
            pdb=" N   ALA L  60 "
            pdb=" C   ALA L  60 "
            pdb=" CB  ALA L  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.67   -0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.51e-01
  ... (remaining 494 not shown)

  Planarity restraints: 590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L  56 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   THR L  56 "    0.034 2.00e-02 2.50e+03
        pdb=" O   THR L  56 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY L  57 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  31 "    0.010 2.00e-02 2.50e+03   1.92e-02 3.69e+00
        pdb=" C   ILE H  31 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ILE H  31 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN H  32 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP H 101 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO H 102 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO H 102 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H 102 "    0.023 5.00e-02 4.00e+02
  ... (remaining 587 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 560
        2.77 -     3.30: 3130
        3.30 -     3.83: 5250
        3.83 -     4.37: 6115
        4.37 -     4.90: 10669
  Nonbonded interactions: 25724
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 367 "
            pdb=" OG  SER A 371 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" NH2 ARG A 457 "
            pdb=" OD2 ASP A 467 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" OH  TYR A 453 "
            pdb=" OE1 GLN A 493 "
     model   vdw
     2.369 3.040
  ... (remaining 25719 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 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:             4.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.590
  Find NCS groups from input model:        0.020
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
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      :  0.009   0.475   3356  Z= 0.457
  Angle     :  0.984  49.602   4562  Z= 0.514
  Chirality :  0.045   0.230    497
  Planarity :  0.004   0.046    589
  Dihedral  : 11.488  61.753   1193
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.02 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.41), residues: 414
  helix: -2.41 (0.71), residues: 38
  sheet: -0.53 (0.53), residues: 110
  loop : -0.60 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  50 
 TYR   0.010   0.001   TYR L  49 
 PHE   0.009   0.001   PHE A 515 
 TRP   0.018   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.20 ( 3349)
  covalent geometry    : angle       0.58682 /  0.35 ( 4547)
  SS BOND              : bond        0.19373 / 10.20 (    6)
  SS BOND              : angle      15.41414 /  8.81 (   12)
  hydrogen bonds       : bond        0.28302 / 17.57 (   82)
  hydrogen bonds       : angle      12.28426 /  8.58 (  207)
  link_NAG-ASN         : bond        0.00233 /  0.12 (    1)
  link_NAG-ASN         : angle       1.13577 /  0.53 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.8021 (t80) cc_final: 0.7525 (t80)
REVERT: A  368 LEU cc_start: 0.5658 (mm) cc_final: 0.5447 (mm)
REVERT: A  458 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8652 (mmtm)
REVERT: A  507 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8078 (Cg_endo)
REVERT: H   10 GLU cc_start: 0.3299 (tt0) cc_final: 0.3026 (mt-10)
REVERT: H   29 PHE cc_start: 0.7177 (m-80) cc_final: 0.6948 (m-10)
REVERT: H   46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: H   79 TYR cc_start: 0.7709 (m-80) cc_final: 0.6961 (m-80)
REVERT: L    4 MET cc_start: 0.7409 (mmm) cc_final: 0.6974 (tpp)
REVERT: L   18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7001 (tpp-160)
REVERT: L   36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8422 (m-10)
REVERT: L   49 TYR cc_start: 0.8499 (p90) cc_final: 0.8086 (p90)
REVERT: L   87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8133 (m-10)
  outliers start: 9
  outliers final: 3
  residues processed: 139
  average time/residue: 0.0860
  time to fit residues: 13.8941
Evaluate side-chains
  105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain L residue    3 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  61 GLN
L  79 GLN
** L  89 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.138988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.123046 restraints weight = 7122.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.126350 restraints weight = 4160.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.128674 restraints weight = 2808.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130354 restraints weight = 2079.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.131410 restraints weight = 1634.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3356  Z= 0.146
  Angle     :  0.592   5.062   4562  Z= 0.313
  Chirality :  0.046   0.163    497
  Planarity :  0.006   0.057    589
  Dihedral  :  4.812  39.310    469
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 17.80 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.40), residues: 414
  helix: -1.79 (0.80), residues: 37
  sheet: -0.09 (0.54), residues: 97
  loop : -0.85 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  61 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.014   0.002   PHE A 464 
 TRP   0.010   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 ( 3349)
  covalent geometry    : angle       0.58978 /  0.31 ( 4547)
  SS BOND              : bond        0.00644 /  0.33 (    6)
  SS BOND              : angle       1.04353 /  0.60 (   12)
  hydrogen bonds       : bond        0.04543 /  3.01 (   82)
  hydrogen bonds       : angle       8.27893 /  5.73 (  207)
  link_NAG-ASN         : bond        0.00183 /  0.10 (    1)
  link_NAG-ASN         : angle       1.07333 /  0.49 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.7936 (ttt90) cc_final: 0.6977 (ttm170)
REVERT: A  464 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6278 (t80)
REVERT: A  474 GLN cc_start: 0.6315 (mt0) cc_final: 0.5885 (mm-40)
REVERT: A  507 PRO cc_start: 0.8146 (Cg_exo) cc_final: 0.7869 (Cg_endo)
REVERT: A  509 ARG cc_start: 0.8718 (ptp-170) cc_final: 0.8318 (mtp180)
REVERT: H   29 PHE cc_start: 0.7091 (m-80) cc_final: 0.6873 (m-10)
REVERT: H   79 TYR cc_start: 0.7394 (m-80) cc_final: 0.6712 (m-80)
REVERT: L    4 MET cc_start: 0.7491 (mmm) cc_final: 0.7122 (tpp)
REVERT: L   11 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7149 (tm)
REVERT: L   18 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7001 (tpp-160)
  outliers start: 17
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0696
  time to fit residues: 8.9345
Evaluate side-chains
  101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
H   6 GLN
H  61 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  93 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.123035 restraints weight = 7212.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.126354 restraints weight = 4306.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.128716 restraints weight = 2971.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.130279 restraints weight = 2234.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131497 restraints weight = 1803.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3356  Z= 0.141
  Angle     :  0.599   6.890   4562  Z= 0.307
  Chirality :  0.046   0.176    497
  Planarity :  0.005   0.047    589
  Dihedral  :  4.752  40.254    467
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 18.64 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.40), residues: 414
  helix: -1.64 (0.86), residues: 37
  sheet: -0.20 (0.52), residues: 96
  loop : -0.80 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.013   0.001   TYR H  47 
 PHE   0.015   0.001   PHE A 338 
 TRP   0.004   0.001   TRP A 353 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 3349)
  covalent geometry    : angle       0.59762 /  0.31 ( 4547)
  SS BOND              : bond        0.00230 /  0.15 (    6)
  SS BOND              : angle       0.74677 /  0.43 (   12)
  hydrogen bonds       : bond        0.03802 /  2.52 (   82)
  hydrogen bonds       : angle       7.33237 /  5.05 (  207)
  link_NAG-ASN         : bond        0.00185 /  0.10 (    1)
  link_NAG-ASN         : angle       1.28655 /  0.58 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 ARG cc_start: 0.8241 (ttt90) cc_final: 0.6829 (ttm170)
REVERT: A  464 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6089 (t80)
REVERT: A  474 GLN cc_start: 0.6208 (mt0) cc_final: 0.5821 (mm-40)
REVERT: H   79 TYR cc_start: 0.7381 (m-80) cc_final: 0.6752 (m-80)
REVERT: L    4 MET cc_start: 0.7493 (mmm) cc_final: 0.7148 (tpp)
REVERT: L   11 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7138 (tm)
REVERT: L   18 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.6896 (tpp-160)
  outliers start: 21
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0677
  time to fit residues: 8.5668
Evaluate side-chains
  103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0170
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  61 GLN
L  79 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.141244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.124622 restraints weight = 6989.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.127956 restraints weight = 4212.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.130289 restraints weight = 2926.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.131921 restraints weight = 2211.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132947 restraints weight = 1773.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3356  Z= 0.144
  Angle     :  0.575   5.149   4562  Z= 0.296
  Chirality :  0.045   0.185    497
  Planarity :  0.005   0.054    589
  Dihedral  :  4.785  40.371    467
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 18.93 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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 (0.41), residues: 414
  helix: -1.61 (0.97), residues: 32
  sheet: -0.07 (0.52), residues: 94
  loop : -0.72 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 346 
 TYR   0.014   0.001   TYR H  47 
 PHE   0.013   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 3349)
  covalent geometry    : angle       0.57354 /  0.30 ( 4547)
  SS BOND              : bond        0.00244 /  0.14 (    6)
  SS BOND              : angle       0.65114 /  0.37 (   12)
  hydrogen bonds       : bond        0.03504 /  2.33 (   82)
  hydrogen bonds       : angle       6.91982 /  4.80 (  207)
  link_NAG-ASN         : bond        0.00171 /  0.09 (    1)
  link_NAG-ASN         : angle       1.30317 /  0.59 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7880 (t80) cc_final: 0.7401 (t80)
REVERT: A  454 ARG cc_start: 0.7315 (ttp80) cc_final: 0.7093 (ttp80)
REVERT: A  457 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.7450 (ttt90)
REVERT: A  464 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6041 (t80)
REVERT: H   29 PHE cc_start: 0.7069 (m-10) cc_final: 0.6804 (m-10)
REVERT: H   79 TYR cc_start: 0.7288 (m-80) cc_final: 0.6567 (m-80)
REVERT: H   86 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7143 (t70)
REVERT: L    4 MET cc_start: 0.7462 (mmm) cc_final: 0.7139 (tpp)
REVERT: L   11 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7095 (tm)
REVERT: L   18 ARG cc_start: 0.7711 (ttp-170) cc_final: 0.6871 (tpp-160)
  outliers start: 23
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0644
  time to fit residues: 8.4929
Evaluate side-chains
  103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:    0.0470
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 35 optimal weight:    0.0020
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.3486

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  61 GLN
L  79 GLN
L  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.142396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126095 restraints weight = 6877.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.129438 restraints weight = 4079.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.131729 restraints weight = 2823.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133269 restraints weight = 2130.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.134443 restraints weight = 1717.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3356  Z= 0.117
  Angle     :  0.586   6.183   4562  Z= 0.299
  Chirality :  0.046   0.178    497
  Planarity :  0.005   0.045    589
  Dihedral  :  4.661  38.276    467
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 21.75 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.08 (0.40), residues: 414
  helix: -1.67 (0.96), residues: 32
  sheet: -0.22 (0.51), residues: 90
  loop : -0.77 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 346 
 TYR   0.011   0.001   TYR H  47 
 PHE   0.021   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.12 ( 3349)
  covalent geometry    : angle       0.58496 /  0.30 ( 4547)
  SS BOND              : bond        0.00182 /  0.10 (    6)
  SS BOND              : angle       0.54426 /  0.30 (   12)
  hydrogen bonds       : bond        0.03264 /  2.15 (   82)
  hydrogen bonds       : angle       6.74149 /  4.69 (  207)
  link_NAG-ASN         : bond        0.00285 /  0.15 (    1)
  link_NAG-ASN         : angle       1.38566 /  0.63 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6139 (t80)
REVERT: H   79 TYR cc_start: 0.7202 (m-80) cc_final: 0.6514 (m-80)
REVERT: H   86 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7048 (t70)
REVERT: L    4 MET cc_start: 0.7458 (mmm) cc_final: 0.7214 (tpp)
REVERT: L   11 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7146 (tm)
REVERT: L   18 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.6832 (tpp-160)
  outliers start: 23
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0684
  time to fit residues: 8.8375
Evaluate side-chains
  102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   86 ASP
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   91 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.138775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121958 restraints weight = 7123.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125128 restraints weight = 4299.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127491 restraints weight = 3013.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.129141 restraints weight = 2280.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130350 restraints weight = 1830.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3356  Z= 0.221
  Angle     :  0.646   6.013   4562  Z= 0.340
  Chirality :  0.047   0.206    497
  Planarity :  0.006   0.054    589
  Dihedral  :  5.195  41.122    467
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 21.75 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.37 (0.39), residues: 414
  helix: -1.71 (1.03), residues: 26
  sheet: -0.49 (0.48), residues: 107
  loop : -1.02 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 457 
 TYR   0.016   0.002   TYR A 489 
 PHE   0.011   0.002   PHE H 100D
 TRP   0.007   0.002   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00497 /  0.22 ( 3349)
  covalent geometry    : angle       0.64348 /  0.34 ( 4547)
  SS BOND              : bond        0.00293 /  0.15 (    6)
  SS BOND              : angle       0.99555 /  0.53 (   12)
  hydrogen bonds       : bond        0.03756 /  2.47 (   82)
  hydrogen bonds       : angle       6.91497 /  4.86 (  207)
  link_NAG-ASN         : bond        0.00070 /  0.04 (    1)
  link_NAG-ASN         : angle       1.47564 /  0.68 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  509 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8256 (mtp180)
REVERT: H   29 PHE cc_start: 0.7171 (m-10) cc_final: 0.6970 (m-10)
REVERT: H   79 TYR cc_start: 0.7273 (m-80) cc_final: 0.6621 (m-80)
REVERT: L   11 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7294 (tm)
REVERT: L   18 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.6948 (tpp-160)
  outliers start: 24
  outliers final: 18
  residues processed: 105
  average time/residue: 0.0658
  time to fit residues: 8.4412
Evaluate side-chains
  104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   91 TYR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.139952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.123282 restraints weight = 7098.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.126546 restraints weight = 4194.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128923 restraints weight = 2894.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130494 restraints weight = 2171.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.131738 restraints weight = 1746.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.4223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3356  Z= 0.149
  Angle     :  0.616   8.174   4562  Z= 0.315
  Chirality :  0.046   0.192    497
  Planarity :  0.005   0.050    589
  Dihedral  :  4.934  35.686    467
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 23.45 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.40 (0.39), residues: 414
  helix: -1.92 (0.99), residues: 27
  sheet: -0.37 (0.51), residues: 88
  loop : -1.05 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 346 
 TYR   0.012   0.001   TYR A 489 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.004   0.001   TRP H 103 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 3349)
  covalent geometry    : angle       0.61444 /  0.31 ( 4547)
  SS BOND              : bond        0.00295 /  0.17 (    6)
  SS BOND              : angle       0.83578 /  0.44 (   12)
  hydrogen bonds       : bond        0.03424 /  2.26 (   82)
  hydrogen bonds       : angle       6.80934 /  4.78 (  207)
  link_NAG-ASN         : bond        0.00210 /  0.11 (    1)
  link_NAG-ASN         : angle       1.45476 /  0.67 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 PHE cc_start: 0.7852 (t80) cc_final: 0.7231 (t80)
REVERT: A  394 ASN cc_start: 0.7191 (p0) cc_final: 0.6461 (t0)
REVERT: H   79 TYR cc_start: 0.7333 (m-80) cc_final: 0.6684 (m-80)
REVERT: L   11 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7332 (tm)
REVERT: L   18 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.6863 (tpp-160)
  outliers start: 22
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0663
  time to fit residues: 8.7322
Evaluate side-chains
  102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0570
   chunk 19 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6700

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.140048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.123296 restraints weight = 7109.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126562 restraints weight = 4213.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.128926 restraints weight = 2903.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.130672 restraints weight = 2185.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131775 restraints weight = 1734.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3356  Z= 0.157
  Angle     :  0.630   8.983   4562  Z= 0.323
  Chirality :  0.046   0.192    497
  Planarity :  0.005   0.044    589
  Dihedral  :  4.892  30.863    467
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 22.88 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.32 (0.40), residues: 414
  helix: -1.96 (0.98), residues: 27
  sheet: -0.10 (0.51), residues: 101
  loop : -1.10 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.012   0.001   TYR A 489 
 PHE   0.022   0.002   PHE A 338 
 TRP   0.007   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 ( 3349)
  covalent geometry    : angle       0.62722 /  0.32 ( 4547)
  SS BOND              : bond        0.00312 /  0.17 (    6)
  SS BOND              : angle       1.11030 /  0.57 (   12)
  hydrogen bonds       : bond        0.03694 /  2.47 (   82)
  hydrogen bonds       : angle       6.73933 /  4.76 (  207)
  link_NAG-ASN         : bond        0.00225 /  0.12 (    1)
  link_NAG-ASN         : angle       1.61421 /  0.74 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   79 TYR cc_start: 0.7319 (m-80) cc_final: 0.6693 (m-80)
REVERT: L   11 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7291 (tm)
REVERT: L   18 ARG cc_start: 0.7656 (ttp-170) cc_final: 0.6860 (tpp-160)
  outliers start: 22
  outliers final: 21
  residues processed: 99
  average time/residue: 0.0571
  time to fit residues: 6.9572
Evaluate side-chains
  102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    6 GLN
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.141275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124539 restraints weight = 7085.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.127844 restraints weight = 4231.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.130198 restraints weight = 2936.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.131846 restraints weight = 2225.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133051 restraints weight = 1779.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3356  Z= 0.152
  Angle     :  0.662   9.139   4562  Z= 0.339
  Chirality :  0.047   0.228    497
  Planarity :  0.005   0.041    589
  Dihedral  :  4.731  17.094    467
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  6.50 %
    Allowed  : 22.32 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.33 (0.39), residues: 414
  helix: -1.94 (0.99), residues: 26
  sheet: -0.06 (0.51), residues: 101
  loop : -1.14 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.012   0.001   TYR A 489 
 PHE   0.025   0.002   PHE A 338 
 TRP   0.005   0.001   TRP H  36 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 3349)
  covalent geometry    : angle       0.65962 /  0.34 ( 4547)
  SS BOND              : bond        0.00309 /  0.17 (    6)
  SS BOND              : angle       0.97772 /  0.51 (   12)
  hydrogen bonds       : bond        0.03688 /  2.45 (   82)
  hydrogen bonds       : angle       6.76848 /  4.79 (  207)
  link_NAG-ASN         : bond        0.00274 /  0.14 (    1)
  link_NAG-ASN         : angle       1.48908 /  0.68 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 83
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 PHE cc_start: 0.7272 (m-10) cc_final: 0.6958 (m-10)
REVERT: A  509 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8306 (mtp180)
REVERT: H   79 TYR cc_start: 0.7329 (m-80) cc_final: 0.6734 (m-80)
REVERT: L   11 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7313 (tm)
REVERT: L   18 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.6811 (tpp-160)
  outliers start: 23
  outliers final: 20
  residues processed: 97
  average time/residue: 0.0673
  time to fit residues: 7.9207
Evaluate side-chains
  104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 82
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  420 ASP
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  509 ARG
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   70 THR
Chi-restraints excluded: chain H residue   78 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0470
   chunk 29 optimal weight:    0.0060
   chunk 2 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.3494

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.143336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126816 restraints weight = 7023.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.130043 restraints weight = 4185.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.132344 restraints weight = 2909.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.133911 restraints weight = 2203.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.135137 restraints weight = 1781.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3356  Z= 0.129
  Angle     :  0.657   8.881   4562  Z= 0.335
  Chirality :  0.047   0.206    497
  Planarity :  0.005   0.043    589
  Dihedral  :  4.573  15.711    466
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.73 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.27 (0.40), residues: 414
  helix: -2.17 (0.95), residues: 26
  sheet: -0.01 (0.52), residues: 95
  loop : -1.05 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.015   0.001   TYR H  79 
 PHE   0.027   0.002   PHE A 338 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.13 ( 3349)
  covalent geometry    : angle       0.65605 /  0.34 ( 4547)
  SS BOND              : bond        0.00263 /  0.15 (    6)
  SS BOND              : angle       0.81993 /  0.43 (   12)
  hydrogen bonds       : bond        0.03508 /  2.36 (   82)
  hydrogen bonds       : angle       6.61334 /  4.64 (  207)
  link_NAG-ASN         : bond        0.00257 /  0.14 (    1)
  link_NAG-ASN         : angle       1.18408 /  0.54 (    3)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7243 (p0) cc_final: 0.6401 (t0)
REVERT: A  464 PHE cc_start: 0.6465 (t80) cc_final: 0.5986 (t80)
REVERT: H    6 GLN cc_start: 0.7098 (pm20) cc_final: 0.6493 (pm20)
REVERT: H   79 TYR cc_start: 0.7078 (m-80) cc_final: 0.6464 (m-80)
REVERT: L   11 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7342 (tm)
REVERT: L   18 ARG cc_start: 0.7583 (ttp-170) cc_final: 0.6779 (tpp-160)
  outliers start: 17
  outliers final: 14
  residues processed: 95
  average time/residue: 0.0620
  time to fit residues: 7.2824
Evaluate side-chains
  91 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue    7 SER
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   96 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 31 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.142842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.125966 restraints weight = 7139.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.129206 restraints weight = 4193.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131520 restraints weight = 2916.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133047 restraints weight = 2214.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.134303 restraints weight = 1807.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.4901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3356  Z= 0.145
  Angle     :  0.688   8.927   4562  Z= 0.348
  Chirality :  0.047   0.200    497
  Planarity :  0.005   0.041    589
  Dihedral  :  4.611  15.520    466
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 25.42 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -1.29 (0.40), residues: 414
  helix: -2.35 (0.93), residues: 26
  sheet:  0.05 (0.53), residues: 95
  loop : -1.07 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.011   0.001   TYR A 489 
 PHE   0.045   0.002   PHE A 342 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.000   0.000   HIS A 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 ( 3349)
  covalent geometry    : angle       0.68633 /  0.35 ( 4547)
  SS BOND              : bond        0.00297 /  0.18 (    6)
  SS BOND              : angle       1.06681 /  0.57 (   12)
  hydrogen bonds       : bond        0.03675 /  2.43 (   82)
  hydrogen bonds       : angle       6.63002 /  4.67 (  207)
  link_NAG-ASN         : bond        0.00241 /  0.13 (    1)
  link_NAG-ASN         : angle       1.15571 /  0.53 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 881.29 seconds
wall clock time: 15 minutes 50.97 seconds (950.97 seconds total)