Starting phenix.real_space_refine
on Tue Feb  3 21:42:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m3f_63603/02_2026/9m3f_63603.map"
  }
  resolution = 2.79
  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=  -0.000 sd=   0.023
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      38      5.16       5
     C    4494      2.51       5
     N    1181      2.21       5
     O    1347      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7060
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4887
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 2145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2145
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 11, 'TRANS': 258}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.35, per 1000 atoms: 0.19
  Number of scatterers: 7060
  At special positions: 0
  Unit cell: (79.6824, 97.3896, 140.551, 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      38     16.00
     O    1347      8.00
     N    1181      7.00
     C    4494      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.06
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 516 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 529 " - pdb=" SG  CYS B 581 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A  38 "
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 146.1 milliseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1628

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 8 sheets defined
      53.1% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.753A  pdb=" N   LYS A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 103
      removed outlier: 4.059A  pdb=" N   SER A 103 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.637A  pdb=" N   ILE A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.850A  pdb=" N   LYS A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'A' and resid 218 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.824A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 383
      removed outlier: 3.501A  pdb=" N   TYR A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.523A  pdb=" N   SER A 387 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 4.050A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   GLU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.304A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.866A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.816A  pdb=" N   VAL A 560 " --> pdb=" O   GLN A 556 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.725A  pdb=" N   ASN B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.391A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.880A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.312A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 328
      removed outlier: 5.117A  pdb=" N   ASP B 565 " --> pdb=" O   ILE B 578 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.643A  pdb=" N   GLY B 431 " --> pdb=" O   TYR B 380 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   VAL B 433 " --> pdb=" O   GLN B 378 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLN B 378 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362
      removed outlier: 7.110A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 516 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'B' and resid 472 through 475

    350 hydrogen bonds defined for protein.
    999 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: 1.00

  Time building geometry restraints manager: 0.59 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: 1705
        1.33 -     1.45: 1590
        1.45 -     1.58: 3898
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 7253
  Sorted by residual:
  bond pdb=" CA  TYR A 381 "
       pdb=" C   TYR A 381 "
    ideal  model  delta    sigma   weight residual
    1.522  1.445  0.077 1.37e-02 5.33e+03 3.15e+01
  bond pdb=" CA  ALA A 384 "
       pdb=" CB  ALA A 384 "
    ideal  model  delta    sigma   weight residual
    1.536  1.451  0.084 1.65e-02 3.67e+03 2.62e+01
  bond pdb=" N   ASN B 422 "
       pdb=" CA  ASN B 422 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.10e-02 8.26e+03 1.33e+01
  bond pdb=" N   ILE A 468 "
       pdb=" CA  ILE A 468 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 7.70e-03 1.69e+04 1.27e+01
  bond pdb=" N   VAL A 107 "
       pdb=" CA  VAL A 107 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.038 1.08e-02 8.57e+03 1.27e+01
  ... (remaining 7248 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.38: 9708
        3.38 -     6.75: 119
        6.75 -    10.13: 12
       10.13 -    13.50: 2
       13.50 -    16.88: 3
  Bond angle restraints: 9844
  Sorted by residual:
  angle pdb=" N   LEU B 461 "
        pdb=" CA  LEU B 461 "
        pdb=" CB  LEU B 461 "
      ideal   model   delta    sigma   weight residual
     110.23   96.78   13.45 1.62e+00 3.81e-01 6.89e+01
  angle pdb=" CA  TYR A 385 "
        pdb=" CB  TYR A 385 "
        pdb=" CG  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     113.90  127.53  -13.63 1.80e+00 3.09e-01 5.73e+01
  angle pdb=" CG  GLU B 406 "
        pdb=" CD  GLU B 406 "
        pdb=" OE2 GLU B 406 "
      ideal   model   delta    sigma   weight residual
     118.40  135.28  -16.88 2.30e+00 1.89e-01 5.39e+01
  angle pdb=" CA  ASP A 382 "
        pdb=" CB  ASP A 382 "
        pdb=" CG  ASP A 382 "
      ideal   model   delta    sigma   weight residual
     112.60  119.09   -6.49 1.00e+00 1.00e+00 4.22e+01
  angle pdb=" N   TYR A 381 "
        pdb=" CA  TYR A 381 "
        pdb=" C   TYR A 381 "
      ideal   model   delta    sigma   weight residual
     113.23  105.20    8.03 1.24e+00 6.50e-01 4.20e+01
  ... (remaining 9839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3917
       17.95 -    35.90: 309
       35.90 -    53.85: 58
       53.85 -    71.80: 39
       71.80 -    89.75: 3
  Dihedral angle restraints: 4326
    sinusoidal: 1788
      harmonic: 2538
  Sorted by residual:
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -153.98   67.98     1      1.00e+01 1.00e-02 6.00e+01
  dihedral pdb=" CA  GLU A 145 "
           pdb=" C   GLU A 145 "
           pdb=" N   PRO A 146 "
           pdb=" CA  PRO A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -33.22   33.22     0      5.00e+00 4.00e-02 4.41e+01
  dihedral pdb=" N   LEU B 461 "
           pdb=" C   LEU B 461 "
           pdb=" CA  LEU B 461 "
           pdb=" CB  LEU B 461 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.19   15.61     0      2.50e+00 1.60e-01 3.90e+01
  ... (remaining 4323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 635
       0.081 -    0.163: 313
       0.163 -    0.244: 81
       0.244 -    0.325: 6
       0.325 -    0.406: 1
  Chirality restraints: 1036
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-02 2.50e+03 1.50e+02
  chirality pdb=" CA  GLN A 380 "
            pdb=" N   GLN A 380 "
            pdb=" C   GLN A 380 "
            pdb=" CB  GLN A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.13e+00
  chirality pdb=" CA  LEU B 461 "
            pdb=" N   LEU B 461 "
            pdb=" C   LEU B 461 "
            pdb=" CB  LEU B 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.39e+00
  ... (remaining 1033 not shown)

  Planarity restraints: 1273
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.159 2.00e-02 2.50e+03   1.32e-01 2.17e+02
        pdb=" C7  NAG C   1 "   -0.049 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.119 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.211 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 380 "    0.019 2.00e-02 2.50e+03   4.01e-02 1.61e+01
        pdb=" C   GLN A 380 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   GLN A 380 "    0.025 2.00e-02 2.50e+03
        pdb=" N   TYR A 381 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 439 "    0.348 9.50e-02 1.11e+02   1.56e-01 1.50e+01
        pdb=" NE  ARG B 439 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 439 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 439 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 439 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1270 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 42
        2.54 -     3.13: 5447
        3.13 -     3.72: 11132
        3.72 -     4.31: 16282
        4.31 -     4.90: 26527
  Nonbonded interactions: 59430
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 227 "
            pdb=" OH  TYR A 454 "
     model   vdw
     1.949 3.040
  nonbonded pdb=" OD1 ASP A 494 "
            pdb=" OG1 THR A 496 "
     model   vdw
     2.104 3.040
  nonbonded pdb=" O   TYR A 381 "
            pdb=" CD2 TYR A 385 "
     model   vdw
     2.163 3.340
  nonbonded pdb=" OH  TYR A 381 "
            pdb=" CA  GLY A 395 "
     model   vdw
     2.177 3.440
  nonbonded pdb=" OD1 ASP A 382 "
            pdb=" OH  TYR A 385 "
     model   vdw
     2.208 3.040
  ... (remaining 59425 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.610
  Find NCS groups from input model:        0.030
  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:6.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
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      :  0.012   0.084   7262  Z= 0.877
  Angle     :  1.250  16.880   9864  Z= 0.904
  Chirality :  0.091   0.406   1036
  Planarity :  0.009   0.156   1272
  Dihedral  : 14.536  89.755   2677
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.45 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.50 %
    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:  0.56 (0.27), residues: 862
  helix:  0.98 (0.25), residues: 387
  sheet:  0.75 (0.65), residues: 72
  loop : -0.20 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 355 
 TYR   0.038   0.002   TYR A 385 
 PHE   0.009   0.002   PHE B 400 
 TRP   0.014   0.002   TRP B 456 
 HIS   0.008   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.01186 ( 7253)
  covalent geometry    : angle       1.24396 ( 9844)
  SS BOND              : bond        0.00990 (    7)
  SS BOND              : angle       2.25063 (   14)
  hydrogen bonds       : bond        0.17289 (  350)
  hydrogen bonds       : angle       6.76220 (  999)
  link_BETA1-4         : bond        0.04430 (    1)
  link_BETA1-4         : angle       5.12214 (    3)
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       2.67649 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 1
  residues processed: 141
  average time/residue: 0.5969
  time to fit residues: 88.0778
Evaluate side-chains
  66 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0020
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 HIS
A 493 HIS
A 505 HIS
B 394 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.073047 restraints weight = 12362.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.59
r_work: 0.2814 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2681 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   7262  Z= 0.140
  Angle     :  0.593  12.406   9864  Z= 0.311
  Chirality :  0.044   0.155   1036
  Planarity :  0.004   0.043   1272
  Dihedral  :  4.395  33.743    991
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.69 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.28), residues: 862
  helix:  1.84 (0.26), residues: 389
  sheet:  0.77 (0.61), residues: 80
  loop :  0.00 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 429 
 TYR   0.030   0.002   TYR A 385 
 PHE   0.014   0.001   PHE A 230 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 345 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7253)
  covalent geometry    : angle       0.58013 ( 9844)
  SS BOND              : bond        0.00566 (    7)
  SS BOND              : angle       2.74835 (   14)
  hydrogen bonds       : bond        0.04993 (  350)
  hydrogen bonds       : angle       5.25391 (  999)
  link_BETA1-4         : bond        0.00037 (    1)
  link_BETA1-4         : angle       2.33194 (    3)
  link_NAG-ASN         : bond        0.00368 (    1)
  link_NAG-ASN         : angle       3.12998 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 MET cc_start: 0.8872 (mtp) cc_final: 0.8503 (mtm)
REVERT: A  363 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8310 (mttp)
REVERT: A  467 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8057 (mp0)
REVERT: B  334 ASN cc_start: 0.8287 (t0) cc_final: 0.8008 (t0)
REVERT: B  357 ARG cc_start: 0.9050 (ttt-90) cc_final: 0.8844 (ttm-80)
  outliers start: 18
  outliers final: 5
  residues processed: 82
  average time/residue: 0.5263
  time to fit residues: 45.4585
Evaluate side-chains
  66 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  416 LYS
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  433 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 85 optimal weight:   30.0000
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:   30.0000
   chunk 13 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.7358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.102197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.069039 restraints weight = 12381.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 2.62
r_work: 0.2736 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7262  Z= 0.132
  Angle     :  0.631  18.647   9864  Z= 0.323
  Chirality :  0.044   0.294   1036
  Planarity :  0.004   0.047   1272
  Dihedral  :  4.374  38.011    990
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.66 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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:  1.50 (0.28), residues: 862
  helix:  2.02 (0.26), residues: 395
  sheet:  0.67 (0.59), residues: 80
  loop :  0.05 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 429 
 TYR   0.017   0.001   TYR B 369 
 PHE   0.012   0.001   PHE A 523 
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7253)
  covalent geometry    : angle       0.59740 ( 9844)
  SS BOND              : bond        0.00802 (    7)
  SS BOND              : angle       5.11625 (   14)
  hydrogen bonds       : bond        0.04970 (  350)
  hydrogen bonds       : angle       5.02416 (  999)
  link_BETA1-4         : bond        0.00474 (    1)
  link_BETA1-4         : angle       2.18109 (    3)
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       3.16234 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  137 ASN cc_start: 0.8260 (t0) cc_final: 0.7940 (p0)
REVERT: A  332 MET cc_start: 0.9480 (ttp) cc_final: 0.9276 (tmm)
REVERT: A  467 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8129 (mp0)
REVERT: B  334 ASN cc_start: 0.8331 (t0) cc_final: 0.8036 (t0)
REVERT: B  408 ARG cc_start: 0.8975 (ppt170) cc_final: 0.8716 (ppt170)
  outliers start: 16
  outliers final: 7
  residues processed: 78
  average time/residue: 0.4625
  time to fit residues: 38.2292
Evaluate side-chains
  66 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
A 401 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.100764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.067693 restraints weight = 12440.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.58
r_work: 0.2779 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2643 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7262  Z= 0.124
  Angle     :  0.606  16.587   9864  Z= 0.307
  Chirality :  0.043   0.221   1036
  Planarity :  0.004   0.047   1272
  Dihedral  :  4.162  36.319    990
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 14.40 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.48 (0.28), residues: 862
  helix:  1.94 (0.25), residues: 402
  sheet:  0.42 (0.56), residues: 80
  loop :  0.16 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 429 
 TYR   0.020   0.001   TYR B 369 
 PHE   0.012   0.001   PHE A 523 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7253)
  covalent geometry    : angle       0.57576 ( 9844)
  SS BOND              : bond        0.00499 (    7)
  SS BOND              : angle       4.77987 (   14)
  hydrogen bonds       : bond        0.04673 (  350)
  hydrogen bonds       : angle       4.75541 (  999)
  link_BETA1-4         : bond        0.00041 (    1)
  link_BETA1-4         : angle       2.18960 (    3)
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       2.92830 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASN cc_start: 0.8160 (t0) cc_final: 0.7954 (t0)
REVERT: A  467 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (mt-10)
REVERT: B  334 ASN cc_start: 0.8354 (t0) cc_final: 0.8047 (t0)
  outliers start: 21
  outliers final: 9
  residues processed: 85
  average time/residue: 0.4647
  time to fit residues: 42.0691
Evaluate side-chains
  72 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 70 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.099213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.065567 restraints weight = 12546.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 2.61
r_work: 0.2734 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7262  Z= 0.135
  Angle     :  0.604  14.057   9864  Z= 0.307
  Chirality :  0.042   0.199   1036
  Planarity :  0.004   0.048   1272
  Dihedral  :  4.150  36.422    990
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.40 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.48 (0.28), residues: 862
  helix:  1.94 (0.25), residues: 402
  sheet:  0.34 (0.56), residues: 80
  loop :  0.18 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 429 
 TYR   0.015   0.001   TYR A 516 
 PHE   0.014   0.001   PHE A 523 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7253)
  covalent geometry    : angle       0.57532 ( 9844)
  SS BOND              : bond        0.00665 (    7)
  SS BOND              : angle       4.58339 (   14)
  hydrogen bonds       : bond        0.04879 (  350)
  hydrogen bonds       : angle       4.71171 (  999)
  link_BETA1-4         : bond        0.00071 (    1)
  link_BETA1-4         : angle       2.17750 (    3)
  link_NAG-ASN         : bond        0.00189 (    1)
  link_NAG-ASN         : angle       3.22451 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7907 (tp30)
REVERT: A  137 ASN cc_start: 0.8002 (t0) cc_final: 0.7740 (t0)
REVERT: A  190 MET cc_start: 0.8846 (ttp) cc_final: 0.8626 (ttt)
REVERT: A  363 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8635 (mttp)
REVERT: A  467 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8530 (mt-10)
REVERT: B  334 ASN cc_start: 0.8399 (t0) cc_final: 0.8098 (t0)
  outliers start: 19
  outliers final: 9
  residues processed: 80
  average time/residue: 0.4811
  time to fit residues: 40.8693
Evaluate side-chains
  72 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0470
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.099425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.066011 restraints weight = 12588.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2884 rms_B_bonded: 2.61
r_work: 0.2744 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2607 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7262  Z= 0.121
  Angle     :  0.587  13.919   9864  Z= 0.299
  Chirality :  0.042   0.195   1036
  Planarity :  0.004   0.048   1272
  Dihedral  :  4.040  38.331    990
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.43 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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:  1.49 (0.28), residues: 862
  helix:  1.96 (0.25), residues: 402
  sheet:  0.34 (0.56), residues: 80
  loop :  0.17 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 429 
 TYR   0.015   0.001   TYR B 369 
 PHE   0.016   0.001   PHE B 392 
 TRP   0.008   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7253)
  covalent geometry    : angle       0.56030 ( 9844)
  SS BOND              : bond        0.00551 (    7)
  SS BOND              : angle       4.33978 (   14)
  hydrogen bonds       : bond        0.04646 (  350)
  hydrogen bonds       : angle       4.61885 (  999)
  link_BETA1-4         : bond        0.00066 (    1)
  link_BETA1-4         : angle       2.13160 (    3)
  link_NAG-ASN         : bond        0.00143 (    1)
  link_NAG-ASN         : angle       3.03621 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8013 (tp30)
REVERT: A  137 ASN cc_start: 0.8019 (t0) cc_final: 0.7692 (t0)
REVERT: A  190 MET cc_start: 0.8869 (ttp) cc_final: 0.8604 (ttt)
REVERT: A  363 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8554 (mttm)
REVERT: A  401 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.8314 (m-70)
REVERT: A  467 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8552 (mt-10)
REVERT: B  334 ASN cc_start: 0.8506 (t0) cc_final: 0.8181 (t0)
REVERT: B  408 ARG cc_start: 0.8871 (ptt90) cc_final: 0.8345 (ppt170)
  outliers start: 19
  outliers final: 10
  residues processed: 79
  average time/residue: 0.4741
  time to fit residues: 39.7469
Evaluate side-chains
  74 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  344 CYS
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 63 optimal weight:    7.9990
   chunk 40 optimal weight:    0.0870
   chunk 77 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
B 478 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.099480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.066527 restraints weight = 12457.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.56
r_work: 0.2754 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2617 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7262  Z= 0.116
  Angle     :  0.579  14.001   9864  Z= 0.292
  Chirality :  0.041   0.184   1036
  Planarity :  0.004   0.048   1272
  Dihedral  :  3.956  40.618    990
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.21 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.51 (0.28), residues: 862
  helix:  1.97 (0.25), residues: 404
  sheet:  0.11 (0.62), residues: 70
  loop :  0.22 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 429 
 TYR   0.017   0.001   TYR B 369 
 PHE   0.018   0.001   PHE B 392 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7253)
  covalent geometry    : angle       0.55480 ( 9844)
  SS BOND              : bond        0.00681 (    7)
  SS BOND              : angle       4.13834 (   14)
  hydrogen bonds       : bond        0.04546 (  350)
  hydrogen bonds       : angle       4.56763 (  999)
  link_BETA1-4         : bond        0.00161 (    1)
  link_BETA1-4         : angle       2.03156 (    3)
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       3.03638 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8015 (tp30)
REVERT: A  137 ASN cc_start: 0.8138 (t0) cc_final: 0.7794 (t0)
REVERT: A  363 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8587 (mttm)
REVERT: A  467 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8547 (mt-10)
REVERT: B  334 ASN cc_start: 0.8490 (t0) cc_final: 0.7960 (p0)
  outliers start: 19
  outliers final: 11
  residues processed: 85
  average time/residue: 0.4939
  time to fit residues: 44.4441
Evaluate side-chains
  73 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.097726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.065108 restraints weight = 12433.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.50
r_work: 0.2717 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2580 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7262  Z= 0.137
  Angle     :  0.601  14.503   9864  Z= 0.304
  Chirality :  0.042   0.187   1036
  Planarity :  0.004   0.049   1272
  Dihedral  :  4.029  40.746    990
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.51 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.56 (0.28), residues: 862
  helix:  1.99 (0.25), residues: 402
  sheet:  0.21 (0.62), residues: 70
  loop :  0.27 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 429 
 TYR   0.015   0.001   TYR A 516 
 PHE   0.017   0.001   PHE B 392 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7253)
  covalent geometry    : angle       0.57618 ( 9844)
  SS BOND              : bond        0.00765 (    7)
  SS BOND              : angle       4.18288 (   14)
  hydrogen bonds       : bond        0.04821 (  350)
  hydrogen bonds       : angle       4.59089 (  999)
  link_BETA1-4         : bond        0.00072 (    1)
  link_BETA1-4         : angle       2.17083 (    3)
  link_NAG-ASN         : bond        0.00334 (    1)
  link_NAG-ASN         : angle       3.42225 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8035 (tp30)
REVERT: A  137 ASN cc_start: 0.8196 (t0) cc_final: 0.7782 (t0)
REVERT: A  363 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8601 (mttm)
REVERT: A  467 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8539 (mt-10)
REVERT: B  334 ASN cc_start: 0.8553 (t0) cc_final: 0.8350 (t0)
REVERT: B  386 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8945 (mtmm)
REVERT: B  408 ARG cc_start: 0.8866 (ptt90) cc_final: 0.8421 (ppt170)
  outliers start: 15
  outliers final: 11
  residues processed: 76
  average time/residue: 0.5371
  time to fit residues: 43.0746
Evaluate side-chains
  72 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 54 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.097829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.065344 restraints weight = 12319.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.46
r_work: 0.2734 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2601 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7262  Z= 0.129
  Angle     :  0.581  14.299   9864  Z= 0.295
  Chirality :  0.042   0.180   1036
  Planarity :  0.004   0.049   1272
  Dihedral  :  3.978  40.817    990
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.25 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.58 (0.28), residues: 862
  helix:  1.98 (0.25), residues: 403
  sheet:  0.22 (0.62), residues: 70
  loop :  0.32 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 429 
 TYR   0.016   0.001   TYR B 369 
 PHE   0.017   0.001   PHE B 392 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7253)
  covalent geometry    : angle       0.55647 ( 9844)
  SS BOND              : bond        0.00664 (    7)
  SS BOND              : angle       4.06021 (   14)
  hydrogen bonds       : bond        0.04716 (  350)
  hydrogen bonds       : angle       4.57457 (  999)
  link_BETA1-4         : bond        0.00177 (    1)
  link_BETA1-4         : angle       2.17864 (    3)
  link_NAG-ASN         : bond        0.00280 (    1)
  link_NAG-ASN         : angle       3.39411 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8026 (tp30)
REVERT: A  137 ASN cc_start: 0.8265 (t0) cc_final: 0.7859 (t0)
REVERT: A  363 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8619 (mttm)
REVERT: A  467 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8539 (mt-10)
REVERT: B  386 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8936 (mtmm)
  outliers start: 15
  outliers final: 10
  residues processed: 74
  average time/residue: 0.5619
  time to fit residues: 43.8626
Evaluate side-chains
  70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 54 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:   40.0000
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.098071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.065435 restraints weight = 12406.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 2.48
r_work: 0.2738 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7262  Z= 0.124
  Angle     :  0.584  14.495   9864  Z= 0.296
  Chirality :  0.042   0.165   1036
  Planarity :  0.004   0.048   1272
  Dihedral  :  3.938  40.364    990
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 18.03 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.62 (0.28), residues: 862
  helix:  1.96 (0.25), residues: 409
  sheet:  0.23 (0.62), residues: 70
  loop :  0.38 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 429 
 TYR   0.016   0.001   TYR B 369 
 PHE   0.017   0.001   PHE B 392 
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7253)
  covalent geometry    : angle       0.56116 ( 9844)
  SS BOND              : bond        0.00645 (    7)
  SS BOND              : angle       3.90779 (   14)
  hydrogen bonds       : bond        0.04622 (  350)
  hydrogen bonds       : angle       4.53147 (  999)
  link_BETA1-4         : bond        0.00200 (    1)
  link_BETA1-4         : angle       2.11906 (    3)
  link_NAG-ASN         : bond        0.00258 (    1)
  link_NAG-ASN         : angle       3.41676 (    3)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8008 (tp30)
REVERT: A  137 ASN cc_start: 0.8237 (t0) cc_final: 0.7804 (t0)
REVERT: A  332 MET cc_start: 0.9474 (ttp) cc_final: 0.9234 (ttp)
REVERT: A  363 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8598 (mttm)
REVERT: A  467 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8506 (mt-10)
REVERT: B  334 ASN cc_start: 0.7927 (t0) cc_final: 0.7501 (p0)
REVERT: B  386 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8947 (mtmm)
REVERT: B  408 ARG cc_start: 0.8802 (ptt90) cc_final: 0.8391 (ppt170)
  outliers start: 14
  outliers final: 11
  residues processed: 72
  average time/residue: 0.5333
  time to fit residues: 40.6525
Evaluate side-chains
  71 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  250 ASP
Chi-restraints excluded: chain A residue  363 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  467 GLU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  373 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  477 THR
Chi-restraints excluded: chain B residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0770
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7944

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.097607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.064973 restraints weight = 12314.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.48
r_work: 0.2730 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2595 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.4362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7262  Z= 0.130
  Angle     :  0.587  14.382   9864  Z= 0.297
  Chirality :  0.042   0.163   1036
  Planarity :  0.004   0.047   1272
  Dihedral  :  3.922  40.363    990
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.64 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  1.64 (0.28), residues: 862
  helix:  1.97 (0.25), residues: 409
  sheet:  0.24 (0.62), residues: 70
  loop :  0.40 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 429 
 TYR   0.016   0.001   TYR B 369 
 PHE   0.017   0.001   PHE B 392 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7253)
  covalent geometry    : angle       0.56421 ( 9844)
  SS BOND              : bond        0.00646 (    7)
  SS BOND              : angle       3.87007 (   14)
  hydrogen bonds       : bond        0.04697 (  350)
  hydrogen bonds       : angle       4.53414 (  999)
  link_BETA1-4         : bond        0.00182 (    1)
  link_BETA1-4         : angle       2.16771 (    3)
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       3.60390 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2476.68 seconds
wall clock time: 42 minutes 50.61 seconds (2570.61 seconds total)