Starting phenix.real_space_refine
on Sat Aug 23 08:47:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xyz_38784/08_2025/8xyz_38784.map"
  }
  resolution = 2.96
  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=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5732 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4112      2.51       5
     N    1067      2.21       5
     O    1212      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6429
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 4885
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4885
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 29, 'TRANS': 566}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.15, per 1000 atoms: 0.18
  Number of scatterers: 6429
  At special positions: 0
  Unit cell: (75.21, 86.25, 122.13, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1212      8.00
     N    1067      7.00
     C    4112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.43
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.63

  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
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 370.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      57.4% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.535A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 372
      removed outlier: 4.291A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ALA B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.211A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE B 410 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.574A  pdb=" N   ASP B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 4.163A  pdb=" N   GLU A  38 " --> pdb=" O   TYR A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 4.149A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A 108 " --> pdb=" O   SER A 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 104 through 108'
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.528A  pdb=" N   ALA A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.567A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 3.869A  pdb=" N   ASP A 224 " --> pdb=" O   ASN A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 4.142A  pdb=" N   ASP A 250 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   THR A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    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 283
      removed outlier: 3.563A  pdb=" N   TYR A 279 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      removed outlier: 4.010A  pdb=" N   VAL A 283 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.761A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 4.545A  pdb=" N   HIS A 401 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   GLU A 402 " --> pdb=" O   GLU A 398 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 466
      removed outlier: 3.637A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   THR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    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 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
      removed outlier: 3.615A  pdb=" N   ALA A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.486A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLN A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.509A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.754A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU A 560 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.580A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.599A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.667A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.600A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.736A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)

    301 hydrogen bonds defined for protein.
    876 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: 0.89

  Time building geometry restraints manager: 0.65 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: 1661
        1.33 -     1.45: 1413
        1.45 -     1.57: 3481
        1.57 -     1.69: 1
        1.69 -     1.81: 58
  Bond restraints: 6614
  Sorted by residual:
  bond pdb=" C   TYR A 215 "
       pdb=" N   ASN A 216 "
    ideal  model  delta    sigma   weight residual
    1.330  1.226  0.103 1.37e-02 5.33e+03 5.68e+01
  bond pdb=" C   ASN A 216 "
       pdb=" N   TYR A 217 "
    ideal  model  delta    sigma   weight residual
    1.331  1.254  0.077 1.30e-02 5.92e+03 3.53e+01
  bond pdb=" C   TYR A  83 "
       pdb=" N   PRO A  84 "
    ideal  model  delta    sigma   weight residual
    1.331  1.389 -0.058 1.27e-02 6.20e+03 2.08e+01
  bond pdb=" CA  LYS B 386 "
       pdb=" C   LYS B 386 "
    ideal  model  delta    sigma   weight residual
    1.526  1.577 -0.051 1.29e-02 6.01e+03 1.57e+01
  bond pdb=" CA  TYR A  83 "
       pdb=" C   TYR A  83 "
    ideal  model  delta    sigma   weight residual
    1.523  1.568 -0.045 1.19e-02 7.06e+03 1.42e+01
  ... (remaining 6609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 8685
        2.38 -     4.77: 226
        4.77 -     7.15: 47
        7.15 -     9.54: 25
        9.54 -    11.92: 8
  Bond angle restraints: 8991
  Sorted by residual:
  angle pdb=" N   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" C   TYR B 495 "
      ideal   model   delta    sigma   weight residual
     111.36  121.55  -10.19 1.09e+00 8.42e-01 8.75e+01
  angle pdb=" N   ALA B 520 "
        pdb=" CA  ALA B 520 "
        pdb=" C   ALA B 520 "
      ideal   model   delta    sigma   weight residual
     108.25   97.62   10.63 1.16e+00 7.43e-01 8.39e+01
  angle pdb=" N   THR B 523 "
        pdb=" CA  THR B 523 "
        pdb=" C   THR B 523 "
      ideal   model   delta    sigma   weight residual
     111.07  119.59   -8.52 1.07e+00 8.73e-01 6.33e+01
  angle pdb=" N   LEU A 591 "
        pdb=" CA  LEU A 591 "
        pdb=" C   LEU A 591 "
      ideal   model   delta    sigma   weight residual
     111.36  103.01    8.35 1.09e+00 8.42e-01 5.86e+01
  angle pdb=" N   THR A  82 "
        pdb=" CA  THR A  82 "
        pdb=" C   THR A  82 "
      ideal   model   delta    sigma   weight residual
     111.28  119.42   -8.14 1.09e+00 8.42e-01 5.57e+01
  ... (remaining 8986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 3222
       17.40 -    34.81: 468
       34.81 -    52.21: 154
       52.21 -    69.61: 36
       69.61 -    87.02: 13
  Dihedral angle restraints: 3893
    sinusoidal: 1566
      harmonic: 2327
  Sorted by residual:
  dihedral pdb=" N   CYS B 525 "
           pdb=" C   CYS B 525 "
           pdb=" CA  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  112.36   10.44     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" N   ASP A 338 "
           pdb=" C   ASP A 338 "
           pdb=" CA  ASP A 338 "
           pdb=" CB  ASP A 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.06  -10.26     0      2.50e+00 1.60e-01 1.68e+01
  dihedral pdb=" C   GLU A 145 "
           pdb=" N   GLU A 145 "
           pdb=" CA  GLU A 145 "
           pdb=" CB  GLU A 145 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.52    9.92     0      2.50e+00 1.60e-01 1.57e+01
  ... (remaining 3890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 829
       0.094 -    0.188: 74
       0.188 -    0.283: 20
       0.283 -    0.377: 7
       0.377 -    0.471: 3
  Chirality restraints: 933
  Sorted by residual:
  chirality pdb=" CA  GLU A 145 "
            pdb=" N   GLU A 145 "
            pdb=" C   GLU A 145 "
            pdb=" CB  GLU A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.54e+00
  chirality pdb=" CA  ASP A 338 "
            pdb=" N   ASP A 338 "
            pdb=" C   ASP A 338 "
            pdb=" CB  ASP A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" CA  THR A  82 "
            pdb=" N   THR A  82 "
            pdb=" C   THR A  82 "
            pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.11    0.41 2.00e-01 2.50e+01 4.29e+00
  ... (remaining 930 not shown)

  Planarity restraints: 1166
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 524 "   -0.012 2.00e-02 2.50e+03   2.45e-02 6.00e+00
        pdb=" C   VAL B 524 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL B 524 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   CYS B 525 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 209 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.56e+00
        pdb=" CD  GLU A 209 "    0.041 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 209 "   -0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 209 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 335 "    0.039 5.00e-02 4.00e+02   5.74e-02 5.28e+00
        pdb=" N   PRO A 336 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 336 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 336 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1163 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 93
        2.62 -     3.19: 5637
        3.19 -     3.76: 9504
        3.76 -     4.33: 12327
        4.33 -     4.90: 20435
  Nonbonded interactions: 47996
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.056 2.230
  nonbonded pdb=" OD1 ASP A 303 "
            pdb=" N   ALA A 304 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" O   ASN A 194 "
            pdb=" OD1 ASN A 194 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER A 109 "
            pdb=" OD1 ASP A 111 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" ND2 ASN B 334 "
            pdb=" O   ASN B 360 "
     model   vdw
     2.292 3.120
  ... (remaining 47991 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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.610
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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      :  0.011   0.599   6618  Z= 0.554
  Angle     :  1.093  26.879   8995  Z= 0.679
  Chirality :  0.069   0.471    933
  Planarity :  0.006   0.083   1166
  Dihedral  : 19.008  87.018   2395
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  1.91 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 40.11 %
    Favored  : 58.02 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.29), residues: 787
  helix:  1.73 (0.26), residues: 397
  sheet:  2.02 (0.82), residues: 31
  loop : -0.75 (0.29), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 115 
 TYR   0.026   0.002   TYR A 521 
 PHE   0.026   0.002   PHE A 314 
 TRP   0.016   0.001   TRP B 353 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 6614)
  covalent geometry    : angle       1.02092 ( 8991)
  SS BOND              : bond        0.50701 (    2)
  SS BOND              : angle      18.48355 (    4)
  hydrogen bonds       : bond        0.17893 (  301)
  hydrogen bonds       : angle       5.71856 (  876)
  metal coordination   : bond        0.17321 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 211
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A  194 ASN cc_start: 0.7989 (t0) cc_final: 0.7747 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 218
  average time/residue: 0.4380
  time to fit residues: 100.8508
Evaluate side-chains
  207 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 200
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  338 ASP
Chi-restraints excluded: chain A residue  339 SER
Chi-restraints excluded: chain A residue  365 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.3244

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

Flipped N/Q/H residues before XYZ refinement:
B 354 ASN
B 409 GLN
B 414 GLN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 501 ASN
A  33 ASN
A  60 GLN
A  96 GLN
A 101 GLN
A 117 ASN
A 134 ASN
A 300 GLN
A 442 GLN
A 535 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.129241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.108384 restraints weight = 10419.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.34
r_work: 0.3313 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6618  Z= 0.178
  Angle     :  0.622   9.206   8995  Z= 0.324
  Chirality :  0.044   0.145    933
  Planarity :  0.005   0.044   1166
  Dihedral  :  5.448  50.313    876
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.16 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 31.52 %
    Favored  : 62.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.29), residues: 787
  helix:  1.96 (0.26), residues: 404
  sheet:  1.94 (0.86), residues: 31
  loop : -0.83 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 600 
 TYR   0.015   0.001   TYR A 521 
 PHE   0.017   0.002   PHE B 497 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6614)
  covalent geometry    : angle       0.62163 ( 8991)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       1.22276 (    4)
  hydrogen bonds       : bond        0.07448 (  301)
  hydrogen bonds       : angle       4.44981 (  876)
  metal coordination   : bond        0.00018 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.272 
Fit side-chains
REVERT: B  495 TYR cc_start: 0.8718 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  114 GLN cc_start: 0.8448 (tt0) cc_final: 0.8199 (tt0)
REVERT: A  115 ARG cc_start: 0.8472 (tpm-80) cc_final: 0.8093 (tpm-80)
REVERT: A  131 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (mmtm)
REVERT: A  143 LEU cc_start: 0.8379 (mp) cc_final: 0.8101 (mm)
REVERT: A  162 LEU cc_start: 0.8779 (tm) cc_final: 0.8520 (tt)
REVERT: A  181 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8064 (mm-30)
REVERT: A  194 ASN cc_start: 0.8752 (t0) cc_final: 0.8270 (t0)
REVERT: A  435 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7405 (mm-30)
REVERT: A  531 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8395 (tm-30)
REVERT: A  532 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8809 (mm)
REVERT: A  595 LEU cc_start: 0.8611 (mp) cc_final: 0.8397 (mt)
REVERT: A  597 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7787 (mm-30)
REVERT: A  600 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7486 (ttm110)
  outliers start: 42
  outliers final: 12
  residues processed: 208
  average time/residue: 0.4590
  time to fit residues: 100.6738
Evaluate side-chains
  198 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 184
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue  545 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 48 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0770
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
B 422 ASN
B 439 ASN
A 101 GLN
A 300 GLN
A 442 GLN
A 508 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.132658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.111915 restraints weight = 10400.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.39
r_work: 0.3386 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6618  Z= 0.119
  Angle     :  0.542   6.917   8995  Z= 0.279
  Chirality :  0.040   0.142    933
  Planarity :  0.004   0.041   1166
  Dihedral  :  4.512  31.477    869
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 32.95 %
    Favored  : 62.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.30), residues: 787
  helix:  2.04 (0.26), residues: 404
  sheet:  2.21 (0.87), residues: 29
  loop : -0.76 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 600 
 TYR   0.018   0.001   TYR A  50 
 PHE   0.008   0.001   PHE B 374 
 TRP   0.014   0.001   TRP A 163 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 6614)
  covalent geometry    : angle       0.54179 ( 8991)
  SS BOND              : bond        0.00036 (    2)
  SS BOND              : angle       0.56585 (    4)
  hydrogen bonds       : bond        0.05451 (  301)
  hydrogen bonds       : angle       4.08444 (  876)
  metal coordination   : bond        0.00084 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 188
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: B  355 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8084 (ttt180)
REVERT: B  495 TYR cc_start: 0.8633 (m-80) cc_final: 0.8370 (m-80)
REVERT: A  115 ARG cc_start: 0.8383 (tpm-80) cc_final: 0.8159 (tpm-80)
REVERT: A  131 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8460 (mmtm)
REVERT: A  162 LEU cc_start: 0.8756 (tm) cc_final: 0.8491 (tt)
REVERT: A  181 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: A  194 ASN cc_start: 0.8693 (t0) cc_final: 0.8136 (t0)
REVERT: A  297 MET cc_start: 0.8375 (mtt) cc_final: 0.8146 (mtp)
REVERT: A  331 SER cc_start: 0.8720 (p) cc_final: 0.8487 (p)
REVERT: A  435 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7493 (mm-30)
REVERT: A  531 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: A  532 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8650 (mm)
  outliers start: 31
  outliers final: 14
  residues processed: 201
  average time/residue: 0.4220
  time to fit residues: 89.3551
Evaluate side-chains
  212 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 196
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  232 GLN
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  532 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    0.6980
   chunk 50 optimal weight:    0.2980
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0040
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
A  53 ASN
A  58 ASN
A 101 GLN
A 232 GLN
A 300 GLN
A 442 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.132455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.111910 restraints weight = 10405.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 2.34
r_work: 0.3391 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6618  Z= 0.119
  Angle     :  0.538   7.385   8995  Z= 0.275
  Chirality :  0.040   0.137    933
  Planarity :  0.004   0.038   1166
  Dihedral  :  4.113  15.870    865
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 33.52 %
    Favored  : 62.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.30), residues: 787
  helix:  2.04 (0.27), residues: 411
  sheet:  2.00 (0.86), residues: 29
  loop : -0.65 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 600 
 TYR   0.015   0.001   TYR A 385 
 PHE   0.028   0.001   PHE B 497 
 TRP   0.011   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6614)
  covalent geometry    : angle       0.53699 ( 8991)
  SS BOND              : bond        0.00364 (    2)
  SS BOND              : angle       1.47812 (    4)
  hydrogen bonds       : bond        0.05217 (  301)
  hydrogen bonds       : angle       3.95841 (  876)
  metal coordination   : bond        0.00060 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 188
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  495 TYR cc_start: 0.8618 (m-80) cc_final: 0.8302 (m-80)
REVERT: A  115 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8111 (tpm-80)
REVERT: A  131 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8396 (mmtm)
REVERT: A  162 LEU cc_start: 0.8731 (tm) cc_final: 0.8471 (tt)
REVERT: A  181 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8039 (mm-30)
REVERT: A  189 GLU cc_start: 0.8558 (tp30) cc_final: 0.8254 (tp30)
REVERT: A  194 ASN cc_start: 0.8696 (t0) cc_final: 0.8124 (t0)
REVERT: A  435 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7411 (mm-30)
REVERT: A  470 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8583 (ttmt)
REVERT: A  531 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8346 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 204
  average time/residue: 0.4635
  time to fit residues: 99.7011
Evaluate side-chains
  192 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 177
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  300 GLN
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  430 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0050
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
A 101 GLN
A 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.132641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.112011 restraints weight = 10489.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.40
r_work: 0.3375 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6618  Z= 0.125
  Angle     :  0.545   7.955   8995  Z= 0.280
  Chirality :  0.040   0.139    933
  Planarity :  0.004   0.036   1166
  Dihedral  :  4.082  15.366    865
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 33.38 %
    Favored  : 62.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.30), residues: 787
  helix:  2.06 (0.27), residues: 411
  sheet:  1.73 (0.77), residues: 39
  loop : -0.66 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 600 
 TYR   0.016   0.001   TYR A 385 
 PHE   0.032   0.001   PHE B 497 
 TRP   0.013   0.001   TRP A 349 
 HIS   0.003   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6614)
  covalent geometry    : angle       0.54457 ( 8991)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       1.34399 (    4)
  hydrogen bonds       : bond        0.05397 (  301)
  hydrogen bonds       : angle       3.92246 (  876)
  metal coordination   : bond        0.00080 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  495 TYR cc_start: 0.8553 (m-80) cc_final: 0.8271 (m-80)
REVERT: B  497 PHE cc_start: 0.8290 (m-80) cc_final: 0.8025 (m-80)
REVERT: A  115 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8108 (tpm-80)
REVERT: A  131 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (mmtm)
REVERT: A  162 LEU cc_start: 0.8723 (tm) cc_final: 0.8466 (tt)
REVERT: A  181 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7934 (mt-10)
REVERT: A  189 GLU cc_start: 0.8582 (tp30) cc_final: 0.8263 (tp30)
REVERT: A  435 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7408 (mm-30)
REVERT: A  470 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8587 (ttmt)
REVERT: A  531 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8349 (tm-30)
  outliers start: 32
  outliers final: 12
  residues processed: 205
  average time/residue: 0.4639
  time to fit residues: 100.3416
Evaluate side-chains
  195 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  430 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0970
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    0.1980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 409 GLN
A 101 GLN
A 194 ASN
A 300 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.109811 restraints weight = 10441.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.39
r_work: 0.3341 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6618  Z= 0.145
  Angle     :  0.556   8.289   8995  Z= 0.288
  Chirality :  0.042   0.137    933
  Planarity :  0.004   0.035   1166
  Dihedral  :  4.122  15.883    865
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 34.81 %
    Favored  : 61.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.30), residues: 787
  helix:  2.15 (0.27), residues: 404
  sheet:  2.03 (0.83), residues: 29
  loop : -0.75 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 518 
 TYR   0.017   0.001   TYR A 385 
 PHE   0.031   0.001   PHE B 497 
 TRP   0.017   0.001   TRP A 349 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6614)
  covalent geometry    : angle       0.55586 ( 8991)
  SS BOND              : bond        0.00107 (    2)
  SS BOND              : angle       1.21129 (    4)
  hydrogen bonds       : bond        0.06192 (  301)
  hydrogen bonds       : angle       3.97309 (  876)
  metal coordination   : bond        0.00070 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8060 (tt0)
REVERT: B  497 PHE cc_start: 0.8359 (m-80) cc_final: 0.8105 (m-80)
REVERT: A  115 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8165 (tpm-80)
REVERT: A  162 LEU cc_start: 0.8753 (tm) cc_final: 0.8501 (tt)
REVERT: A  189 GLU cc_start: 0.8574 (tp30) cc_final: 0.8193 (tp30)
REVERT: A  435 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7504 (mm-30)
REVERT: A  470 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8651 (ttmt)
REVERT: A  531 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8365 (tm-30)
REVERT: A  580 ASP cc_start: 0.8127 (t0) cc_final: 0.7833 (t0)
  outliers start: 25
  outliers final: 9
  residues processed: 204
  average time/residue: 0.4904
  time to fit residues: 105.7607
Evaluate side-chains
  194 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 183
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  430 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:   40.0000
   chunk 61 optimal weight:    0.7980
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
A 101 GLN
A 117 ASN
A 194 ASN
A 213 ASN
A 300 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.124786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.103977 restraints weight = 10522.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.37
r_work: 0.3250 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6618  Z= 0.273
  Angle     :  0.639   7.660   8995  Z= 0.342
  Chirality :  0.046   0.155    933
  Planarity :  0.004   0.036   1166
  Dihedral  :  4.597  22.446    865
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 33.81 %
    Favored  : 61.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.30), residues: 787
  helix:  1.86 (0.27), residues: 408
  sheet:  1.98 (0.81), residues: 29
  loop : -0.86 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 518 
 TYR   0.022   0.002   TYR A 385 
 PHE   0.029   0.002   PHE B 497 
 TRP   0.018   0.002   TRP A 349 
 HIS   0.006   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 6614)
  covalent geometry    : angle       0.63829 ( 8991)
  SS BOND              : bond        0.00267 (    2)
  SS BOND              : angle       1.61862 (    4)
  hydrogen bonds       : bond        0.08939 (  301)
  hydrogen bonds       : angle       4.45605 (  876)
  metal coordination   : bond        0.00250 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: B  493 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8258 (tt0)
REVERT: B  495 TYR cc_start: 0.8733 (m-80) cc_final: 0.8512 (m-80)
REVERT: A   42 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8248 (mp10)
REVERT: A   92 THR cc_start: 0.8821 (p) cc_final: 0.8613 (m)
REVERT: A  115 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8271 (tpm-80)
REVERT: A  162 LEU cc_start: 0.8846 (tm) cc_final: 0.8592 (tt)
REVERT: A  189 GLU cc_start: 0.8651 (tp30) cc_final: 0.8193 (tp30)
REVERT: A  194 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8424 (t0)
REVERT: A  213 ASN cc_start: 0.8637 (t0) cc_final: 0.8389 (t0)
REVERT: A  282 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8676 (p)
REVERT: A  385 TYR cc_start: 0.8718 (p90) cc_final: 0.8420 (p90)
REVERT: A  435 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: A  470 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8698 (ttmt)
REVERT: A  531 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: A  545 SER cc_start: 0.9270 (OUTLIER) cc_final: 0.8891 (p)
REVERT: A  580 ASP cc_start: 0.8204 (t0) cc_final: 0.7935 (t0)
  outliers start: 33
  outliers final: 13
  residues processed: 212
  average time/residue: 0.4909
  time to fit residues: 109.9607
Evaluate side-chains
  211 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  201 ASP
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  430 GLU
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  607 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 64 optimal weight:    0.1980
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 414 GLN
B 439 ASN
B 481 ASN
A 101 GLN
A 194 ASN
A 300 GLN
A 330 ASN
A 442 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.129575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.108698 restraints weight = 10464.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.39
r_work: 0.3332 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6618  Z= 0.139
  Angle     :  0.593   9.384   8995  Z= 0.311
  Chirality :  0.041   0.138    933
  Planarity :  0.004   0.036   1166
  Dihedral  :  4.360  20.052    865
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 36.39 %
    Favored  : 60.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.30), residues: 787
  helix:  2.01 (0.27), residues: 404
  sheet:  2.02 (0.82), residues: 29
  loop : -0.82 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 192 
 TYR   0.015   0.001   TYR A 385 
 PHE   0.036   0.001   PHE B 497 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6614)
  covalent geometry    : angle       0.59309 ( 8991)
  SS BOND              : bond        0.00298 (    2)
  SS BOND              : angle       1.13329 (    4)
  hydrogen bonds       : bond        0.06141 (  301)
  hydrogen bonds       : angle       4.05307 (  876)
  metal coordination   : bond        0.00103 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.232 
Fit side-chains
REVERT: B  493 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8142 (tt0)
REVERT: B  495 TYR cc_start: 0.8656 (m-80) cc_final: 0.8392 (m-80)
REVERT: A  115 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8169 (tpm-80)
REVERT: A  162 LEU cc_start: 0.8780 (tm) cc_final: 0.8518 (tt)
REVERT: A  189 GLU cc_start: 0.8604 (tp30) cc_final: 0.8205 (tp30)
REVERT: A  194 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (t0)
REVERT: A  213 ASN cc_start: 0.8537 (t0) cc_final: 0.8255 (t0)
REVERT: A  385 TYR cc_start: 0.8366 (p90) cc_final: 0.8089 (p90)
REVERT: A  420 ASN cc_start: 0.8585 (m-40) cc_final: 0.8340 (m-40)
REVERT: A  435 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7477 (mm-30)
REVERT: A  480 MET cc_start: 0.8653 (mtp) cc_final: 0.8452 (mtt)
REVERT: A  531 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: A  580 ASP cc_start: 0.8124 (t0) cc_final: 0.7900 (t0)
REVERT: A  597 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7456 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 201
  average time/residue: 0.4891
  time to fit residues: 103.9723
Evaluate side-chains
  198 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 183
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  589 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
A 101 GLN
A 300 GLN
A 442 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.130845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.110587 restraints weight = 10541.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.36
r_work: 0.3296 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6618  Z= 0.187
  Angle     :  0.623   8.934   8995  Z= 0.324
  Chirality :  0.043   0.136    933
  Planarity :  0.004   0.035   1166
  Dihedral  :  4.376  23.021    865
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 35.96 %
    Favored  : 60.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.30), residues: 787
  helix:  1.99 (0.27), residues: 408
  sheet:  2.02 (0.84), residues: 29
  loop : -0.80 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 518 
 TYR   0.019   0.002   TYR A 385 
 PHE   0.036   0.001   PHE B 497 
 TRP   0.015   0.001   TRP A 349 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6614)
  covalent geometry    : angle       0.62250 ( 8991)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       1.07766 (    4)
  hydrogen bonds       : bond        0.07211 (  301)
  hydrogen bonds       : angle       4.18508 (  876)
  metal coordination   : bond        0.00171 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  495 TYR cc_start: 0.8705 (m-80) cc_final: 0.8393 (m-80)
REVERT: A   92 THR cc_start: 0.8785 (p) cc_final: 0.8577 (m)
REVERT: A  115 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (tpm-80)
REVERT: A  149 ASP cc_start: 0.8060 (m-30) cc_final: 0.7695 (m-30)
REVERT: A  162 LEU cc_start: 0.8802 (tm) cc_final: 0.8554 (tt)
REVERT: A  189 GLU cc_start: 0.8635 (tp30) cc_final: 0.8196 (tp30)
REVERT: A  213 ASN cc_start: 0.8534 (t0) cc_final: 0.8252 (t0)
REVERT: A  385 TYR cc_start: 0.8527 (p90) cc_final: 0.8197 (p90)
REVERT: A  435 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7518 (mm-30)
REVERT: A  531 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8409 (tm-30)
REVERT: A  580 ASP cc_start: 0.8166 (t0) cc_final: 0.7932 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 205
  average time/residue: 0.4067
  time to fit residues: 88.2628
Evaluate side-chains
  206 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 192
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  356 LYS
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  589 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
B 481 ASN
A 101 GLN
A 300 GLN
A 442 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.108939 restraints weight = 10320.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.42
r_work: 0.3334 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6618  Z= 0.145
  Angle     :  0.605   9.864   8995  Z= 0.314
  Chirality :  0.041   0.139    933
  Planarity :  0.004   0.036   1166
  Dihedral  :  4.292  23.484    865
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 36.96 %
    Favored  : 60.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.30), residues: 787
  helix:  1.98 (0.27), residues: 404
  sheet:  2.14 (0.84), residues: 29
  loop : -0.81 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 518 
 TYR   0.037   0.002   TYR B 351 
 PHE   0.035   0.001   PHE B 497 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6614)
  covalent geometry    : angle       0.60498 ( 8991)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.97907 (    4)
  hydrogen bonds       : bond        0.06155 (  301)
  hydrogen bonds       : angle       4.04472 (  876)
  metal coordination   : bond        0.00138 (    2)

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.183 
Fit side-chains
REVERT: B  495 TYR cc_start: 0.8660 (m-80) cc_final: 0.8379 (m-80)
REVERT: A   92 THR cc_start: 0.8717 (p) cc_final: 0.8512 (m)
REVERT: A  115 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8072 (tpm-80)
REVERT: A  162 LEU cc_start: 0.8758 (tm) cc_final: 0.8507 (tt)
REVERT: A  189 GLU cc_start: 0.8605 (tp30) cc_final: 0.8211 (tp30)
REVERT: A  213 ASN cc_start: 0.8450 (t0) cc_final: 0.8176 (t0)
REVERT: A  385 TYR cc_start: 0.8373 (p90) cc_final: 0.8105 (p90)
REVERT: A  435 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7468 (mm-30)
REVERT: A  475 LYS cc_start: 0.8768 (ttpp) cc_final: 0.8434 (ttmm)
REVERT: A  480 MET cc_start: 0.8729 (mtp) cc_final: 0.8527 (mtt)
REVERT: A  531 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8340 (tm-30)
REVERT: A  597 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7417 (tp30)
  outliers start: 19
  outliers final: 10
  residues processed: 198
  average time/residue: 0.4732
  time to fit residues: 99.2591
Evaluate side-chains
  195 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 ASN
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain A residue  115 ARG
Chi-restraints excluded: chain A residue  257 SER
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  530 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    0.3980
   chunk 41 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 439 ASN
B 481 ASN
A 101 GLN
A 300 GLN
A 442 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.109774 restraints weight = 10317.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.38
r_work: 0.3345 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6618  Z= 0.141
  Angle     :  0.611   9.389   8995  Z= 0.315
  Chirality :  0.041   0.132    933
  Planarity :  0.004   0.035   1166
  Dihedral  :  4.216  22.912    865
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 38.25 %
    Favored  : 59.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.30), residues: 787
  helix:  2.01 (0.27), residues: 404
  sheet:  2.15 (0.82), residues: 29
  loop : -0.79 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 518 
 TYR   0.035   0.001   TYR B 351 
 PHE   0.035   0.001   PHE B 497 
 TRP   0.015   0.001   TRP A 163 
 HIS   0.004   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6614)
  covalent geometry    : angle       0.61111 ( 8991)
  SS BOND              : bond        0.00189 (    2)
  SS BOND              : angle       0.93357 (    4)
  hydrogen bonds       : bond        0.05869 (  301)
  hydrogen bonds       : angle       3.99304 (  876)
  metal coordination   : bond        0.00125 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2757.71 seconds
wall clock time: 47 minutes 34.75 seconds (2854.75 seconds total)