Starting phenix.real_space_refine
on Sat Aug 23 07:31:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xn2_38495/08_2025/8xn2_38495.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xn2_38495/08_2025/8xn2_38495.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/8xn2_38495/08_2025/8xn2_38495.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xn2_38495/08_2025/8xn2_38495.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xn2_38495/08_2025/8xn2_38495.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xn2_38495/08_2025/8xn2_38495.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=   0.009
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 4872 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    4175      2.51       5
     N    1074      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  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: 6527
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4987
    Chain: "B"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1545
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A  34 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  34 " occ=0.50
  Time building chain proxies: 2.65, per 1000 atoms: 0.41
  Number of scatterers: 6527
  At special positions: 0
  Unit cell: (84.032, 78.376, 117.968, 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    1240      8.00
     N    1074      7.00
     C    4175      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=2.03
    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=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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 C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A 103 "
      " NAG A 703 " - " ASN A 432 "
      " NAG A 704 " - " ASN A 546 "
      " NAG A 705 " - " ASN A 322 "
      " NAG C   1 " - " ASN A  90 "
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 511.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 706 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 378 "


  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      56.6% alpha, 7.0% 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
      removed outlier: 3.985A  pdb=" N   ASP A  38 " --> pdb=" O  AHIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.693A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.072A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.288A  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 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 3.605A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.644A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.646A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.511A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.077A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    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 484
    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: 4.185A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.580A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 542'
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.525A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 3.891A  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 337 through 342
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 384 through 388
      removed outlier: 3.617A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 384 through 388'
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.760A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134
      removed outlier: 6.967A  pdb=" N   GLU A 140 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.195A  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: 6.467A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.526A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.680A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    925 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: 1.01

  Time building geometry restraints manager: 0.81 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2068
        1.34 -     1.46: 1419
        1.46 -     1.58: 3167
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6712
  Sorted by residual:
  bond pdb=" C   ASN A  33 "
       pdb=" N  BHIS A  34 "
    ideal  model  delta    sigma   weight residual
    1.335  1.393 -0.058 1.38e-02 5.25e+03 1.75e+01
  bond pdb=" N   THR A  20 "
       pdb=" CA  THR A  20 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.031 1.15e-02 7.56e+03 7.42e+00
  bond pdb=" N   GLN A 102 "
       pdb=" CA  GLN A 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.42e-02 4.96e+03 5.47e+00
  bond pdb=" N   LEU A  91 "
       pdb=" CA  LEU A  91 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.03e+00
  bond pdb=" C  BHIS A  34 "
       pdb=" N   GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.334  1.303  0.032 1.43e-02 4.89e+03 4.92e+00
  ... (remaining 6707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 8965
        2.09 -     4.18: 141
        4.18 -     6.27: 20
        6.27 -     8.36: 1
        8.36 -    10.45: 1
  Bond angle restraints: 9128
  Sorted by residual:
  angle pdb=" C   ILE A  21 "
        pdb=" N   GLU A  22 "
        pdb=" CA  GLU A  22 "
      ideal   model   delta    sigma   weight residual
     120.29  109.84   10.45 1.42e+00 4.96e-01 5.42e+01
  angle pdb=" C   ASN A 103 "
        pdb=" N   GLY A 104 "
        pdb=" CA  GLY A 104 "
      ideal   model   delta    sigma   weight residual
     120.14  115.08    5.06 1.25e+00 6.40e-01 1.64e+01
  angle pdb=" C   ASN A  33 "
        pdb=" N  BHIS A  34 "
        pdb=" CA BHIS A  34 "
      ideal   model   delta    sigma   weight residual
     120.31  114.77    5.54 1.52e+00 4.33e-01 1.33e+01
  angle pdb=" N   GLN A 102 "
        pdb=" CA  GLN A 102 "
        pdb=" C   GLN A 102 "
      ideal   model   delta    sigma   weight residual
     113.19  108.90    4.29 1.19e+00 7.06e-01 1.30e+01
  angle pdb=" O   ASN A  33 "
        pdb=" C   ASN A  33 "
        pdb=" N  BHIS A  34 "
      ideal   model   delta    sigma   weight residual
     122.07  125.67   -3.60 1.03e+00 9.43e-01 1.22e+01
  ... (remaining 9123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 3804
       21.15 -    42.31: 212
       42.31 -    63.46: 24
       63.46 -    84.61: 22
       84.61 -   105.77: 5
  Dihedral angle restraints: 4067
    sinusoidal: 1739
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.72   55.72     1      1.00e+01 1.00e-02 4.19e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.90  -32.90     1      1.00e+01 1.00e-02 1.54e+01
  dihedral pdb=" CA  SER B 494 "
           pdb=" C   SER B 494 "
           pdb=" N   TYR B 495 "
           pdb=" CA  TYR B 495 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.169: 973
       0.169 -    0.338: 4
       0.338 -    0.508: 0
       0.508 -    0.677: 1
       0.677 -    0.846: 1
  Chirality restraints: 979
  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   -2.29   -0.11 2.00e-02 2.50e+03 3.08e+01
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 2.85e+01
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.55   -0.85 2.00e-01 2.50e+01 1.79e+01
  ... (remaining 976 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.338 2.00e-02 2.50e+03   2.92e-01 1.06e+03
        pdb=" C7  NAG C   1 "   -0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.048 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.510 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 703 "   -0.307 2.00e-02 2.50e+03   2.64e-01 8.68e+02
        pdb=" C7  NAG A 703 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG A 703 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2  NAG A 703 "    0.450 2.00e-02 2.50e+03
        pdb=" O7  NAG A 703 "   -0.214 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "    0.154 2.00e-02 2.50e+03   1.27e-01 2.02e+02
        pdb=" C7  NAG A 702 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "    0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "   -0.205 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 704
        2.74 -     3.28: 6529
        3.28 -     3.82: 11456
        3.82 -     4.36: 13312
        4.36 -     4.90: 22587
  Nonbonded interactions: 54588
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER B 514 "
            pdb=" OE2 GLU B 516 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 706 "
     model   vdw
     2.275 2.230
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" O   SER B 459 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NE2 HIS A 374 "
            pdb=" OE1 GLU A 402 "
     model   vdw
     2.307 3.120
  ... (remaining 54583 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             15.430
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.180
  Find NCS groups from input model:        0.040
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6033
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.149   6729  Z= 0.222
  Angle     :  0.743  19.143   9166  Z= 0.388
  Chirality :  0.056   0.846    979
  Planarity :  0.013   0.292   1172
  Dihedral  : 14.752 105.768   2552
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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:  1.32 (0.30), residues: 790
  helix:  1.86 (0.27), residues: 394
  sheet:  1.73 (0.79), residues: 37
  loop : -0.30 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 219 
 TYR   0.021   0.001   TYR A 385 
 PHE   0.016   0.001   PHE A 592 
 TRP   0.010   0.001   TRP A 477 
 HIS   0.011   0.002   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6712)
  covalent geometry    : angle       0.63086 ( 9128)
  SS BOND              : bond        0.00122 (    7)
  SS BOND              : angle       0.46252 (   14)
  hydrogen bonds       : bond        0.12362 (  318)
  hydrogen bonds       : angle       5.40144 (  925)
  metal coordination   : bond        0.14462 (    2)
  link_BETA1-4         : bond        0.04267 (    2)
  link_BETA1-4         : angle      10.45151 (    6)
  link_NAG-ASN         : bond        0.01706 (    6)
  link_NAG-ASN         : angle       6.51682 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7381 (mt0) cc_final: 0.7016 (mt0)
REVERT: A   62 MET cc_start: 0.6792 (ttt) cc_final: 0.6481 (ttp)
REVERT: A   63 ASN cc_start: 0.7254 (m-40) cc_final: 0.6920 (m-40)
REVERT: A   69 TRP cc_start: 0.7343 (t-100) cc_final: 0.6981 (t-100)
REVERT: A   79 LEU cc_start: 0.7823 (mt) cc_final: 0.7617 (tt)
REVERT: A  166 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6494 (tm-30)
REVERT: A  249 MET cc_start: 0.6946 (ttm) cc_final: 0.6529 (tmt)
REVERT: A  309 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6684 (tppp)
REVERT: A  315 PHE cc_start: 0.7713 (m-80) cc_final: 0.7427 (m-80)
REVERT: A  320 LEU cc_start: 0.7688 (mt) cc_final: 0.7375 (mp)
REVERT: A  324 THR cc_start: 0.6941 (m) cc_final: 0.6660 (p)
REVERT: A  327 PHE cc_start: 0.6935 (t80) cc_final: 0.6700 (t80)
REVERT: A  330 ASN cc_start: 0.7527 (m-40) cc_final: 0.6911 (m110)
REVERT: A  349 TRP cc_start: 0.7630 (m100) cc_final: 0.7236 (m100)
REVERT: A  362 THR cc_start: 0.6829 (m) cc_final: 0.6107 (m)
REVERT: A  382 ASP cc_start: 0.7116 (m-30) cc_final: 0.6681 (m-30)
REVERT: A  385 TYR cc_start: 0.7179 (p90) cc_final: 0.6884 (p90)
REVERT: A  400 PHE cc_start: 0.7039 (m-10) cc_final: 0.6772 (m-80)
REVERT: A  408 MET cc_start: 0.7077 (mmt) cc_final: 0.6821 (mmt)
REVERT: A  441 LYS cc_start: 0.6470 (tttt) cc_final: 0.6172 (ttpp)
REVERT: A  462 MET cc_start: 0.6474 (mtt) cc_final: 0.5524 (mtm)
REVERT: A  465 LYS cc_start: 0.7999 (mttp) cc_final: 0.7461 (mttt)
REVERT: A  467 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6478 (mp0)
REVERT: A  477 TRP cc_start: 0.5159 (t-100) cc_final: 0.4819 (t-100)
REVERT: A  480 MET cc_start: 0.6110 (mtm) cc_final: 0.5858 (mtp)
REVERT: A  482 ARG cc_start: 0.6322 (ttm170) cc_final: 0.5996 (ttm-80)
REVERT: A  489 GLU cc_start: 0.6397 (pm20) cc_final: 0.5907 (pm20)
REVERT: A  499 ASP cc_start: 0.7568 (m-30) cc_final: 0.7288 (m-30)
REVERT: A  559 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7217 (ppp80)
REVERT: A  562 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7326 (mtmt)
REVERT: A  577 LYS cc_start: 0.7744 (mttp) cc_final: 0.7203 (mtpt)
REVERT: A  582 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6818 (tpm-80)
REVERT: A  603 PHE cc_start: 0.6363 (t80) cc_final: 0.5897 (t80)
REVERT: A  606 TRP cc_start: 0.7584 (p90) cc_final: 0.7199 (p90)
REVERT: A  611 SER cc_start: 0.7182 (m) cc_final: 0.6863 (p)
REVERT: B  407 VAL cc_start: 0.7943 (t) cc_final: 0.7450 (m)
REVERT: B  414 GLN cc_start: 0.7559 (mm110) cc_final: 0.7240 (mm110)
REVERT: B  424 LYS cc_start: 0.7256 (tppt) cc_final: 0.6979 (tttt)
REVERT: B  468 ILE cc_start: 0.7771 (pt) cc_final: 0.7349 (mt)
REVERT: B  512 VAL cc_start: 0.7038 (t) cc_final: 0.6815 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.4921
  time to fit residues: 118.5839
Evaluate side-chains
  179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    0.1980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS    A
A 117 ASN
A 175 GLN
A 194 ASN
A 388 GLN
A 397 ASN
A 493 HIS
A 524 GLN
B 343 ASN
B 437 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.159556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.139239 restraints weight = 19249.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 3.29
r_work: 0.3766 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   6729  Z= 0.276
  Angle     :  0.780  13.032   9166  Z= 0.394
  Chirality :  0.051   0.236    979
  Planarity :  0.005   0.050   1172
  Dihedral  :  8.509  69.967   1026
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 12.23 %
    Favored  : 85.47 %
  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:  0.70 (0.30), residues: 790
  helix:  1.11 (0.25), residues: 400
  sheet:  1.47 (0.70), residues: 34
  loop : -0.30 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 161 
 TYR   0.035   0.003   TYR A 385 
 PHE   0.026   0.003   PHE B 497 
 TRP   0.028   0.003   TRP A 610 
 HIS   0.010   0.002   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 6712)
  covalent geometry    : angle       0.74914 ( 9128)
  SS BOND              : bond        0.00336 (    7)
  SS BOND              : angle       0.67141 (   14)
  hydrogen bonds       : bond        0.05993 (  318)
  hydrogen bonds       : angle       4.82943 (  925)
  metal coordination   : bond        0.00963 (    2)
  link_BETA1-4         : bond        0.01354 (    2)
  link_BETA1-4         : angle       6.99060 (    6)
  link_NAG-ASN         : bond        0.00377 (    6)
  link_NAG-ASN         : angle       2.86145 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.8074 (m-40) cc_final: 0.7707 (m-40)
REVERT: A   68 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8241 (ttmm)
REVERT: A  117 ASN cc_start: 0.8204 (m-40) cc_final: 0.7916 (m110)
REVERT: A  166 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7024 (tm-30)
REVERT: A  309 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7632 (mmmm)
REVERT: A  329 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7328 (tm-30)
REVERT: A  366 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8283 (ttm)
REVERT: A  482 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7636 (ttm170)
REVERT: A  499 ASP cc_start: 0.8010 (m-30) cc_final: 0.7473 (m-30)
REVERT: B  407 VAL cc_start: 0.8797 (t) cc_final: 0.8444 (m)
REVERT: B  449 TYR cc_start: 0.7498 (m-80) cc_final: 0.6968 (m-80)
  outliers start: 16
  outliers final: 4
  residues processed: 203
  average time/residue: 0.4519
  time to fit residues: 97.6053
Evaluate side-chains
  179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 174
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0170
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0070
   chunk 2 optimal weight:    0.1980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 55 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0970
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.1034

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

Flipped N/Q/H residues before XYZ refinement:
** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.162220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.143392 restraints weight = 15215.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.85
r_work: 0.3830 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6729  Z= 0.139
  Angle     :  0.686  15.135   9166  Z= 0.334
  Chirality :  0.045   0.188    979
  Planarity :  0.005   0.047   1172
  Dihedral  :  7.152  55.184   1026
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.84 %
    Favored  : 79.71 %
  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:  0.91 (0.30), residues: 790
  helix:  1.31 (0.25), residues: 395
  sheet:  1.29 (0.72), residues: 44
  loop : -0.23 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 192 
 TYR   0.018   0.002   TYR A 385 
 PHE   0.032   0.002   PHE B 497 
 TRP   0.016   0.001   TRP A 610 
 HIS   0.005   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6712)
  covalent geometry    : angle       0.65212 ( 9128)
  SS BOND              : bond        0.00177 (    7)
  SS BOND              : angle       0.47866 (   14)
  hydrogen bonds       : bond        0.04659 (  318)
  hydrogen bonds       : angle       4.75635 (  925)
  metal coordination   : bond        0.00330 (    2)
  link_BETA1-4         : bond        0.01468 (    2)
  link_BETA1-4         : angle       6.92694 (    6)
  link_NAG-ASN         : bond        0.00309 (    6)
  link_NAG-ASN         : angle       2.74590 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8168 (ttmm)
REVERT: A  131 LYS cc_start: 0.7139 (pttm) cc_final: 0.6793 (pttm)
REVERT: A  166 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6861 (tm-30)
REVERT: A  207 TYR cc_start: 0.8026 (m-80) cc_final: 0.7780 (m-10)
REVERT: A  291 ILE cc_start: 0.7985 (mt) cc_final: 0.7766 (tp)
REVERT: A  329 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7370 (tm-30)
REVERT: A  441 LYS cc_start: 0.7853 (tttt) cc_final: 0.7641 (ttpp)
REVERT: A  571 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6345 (tm-30)
REVERT: B  407 VAL cc_start: 0.8778 (t) cc_final: 0.8466 (m)
REVERT: B  424 LYS cc_start: 0.7883 (tttt) cc_final: 0.7664 (ttpt)
REVERT: B  433 VAL cc_start: 0.7176 (m) cc_final: 0.6802 (p)
REVERT: B  465 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6657 (mt-10)
  outliers start: 17
  outliers final: 4
  residues processed: 180
  average time/residue: 0.5202
  time to fit residues: 98.6253
Evaluate side-chains
  170 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 165
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  349 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0980
   chunk 59 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0000
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 64 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A  58 ASN
A  63 ASN
B 343 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.164323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.144061 restraints weight = 20739.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.49
r_work: 0.3797 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3798
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3798 r_free = 0.3798    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3798
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6729  Z= 0.140
  Angle     :  0.683  14.907   9166  Z= 0.334
  Chirality :  0.044   0.190    979
  Planarity :  0.005   0.044   1172
  Dihedral  :  6.048  57.061   1026
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 21.58 %
    Favored  : 76.69 %
  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:  0.90 (0.30), residues: 790
  helix:  1.40 (0.26), residues: 401
  sheet:  0.78 (0.72), residues: 43
  loop : -0.32 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 466 
 TYR   0.032   0.002   TYR A 183 
 PHE   0.027   0.002   PHE B 377 
 TRP   0.014   0.001   TRP A 610 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6712)
  covalent geometry    : angle       0.65273 ( 9128)
  SS BOND              : bond        0.00138 (    7)
  SS BOND              : angle       0.43938 (   14)
  hydrogen bonds       : bond        0.04481 (  318)
  hydrogen bonds       : angle       4.67860 (  925)
  metal coordination   : bond        0.00252 (    2)
  link_BETA1-4         : bond        0.01381 (    2)
  link_BETA1-4         : angle       6.78015 (    6)
  link_NAG-ASN         : bond        0.00288 (    6)
  link_NAG-ASN         : angle       2.46188 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 167
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8213 (ttmm)
REVERT: A   75 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7768 (mt-10)
REVERT: A  131 LYS cc_start: 0.7067 (pttm) cc_final: 0.6742 (pttm)
REVERT: A  166 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7036 (tm-30)
REVERT: A  329 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A  441 LYS cc_start: 0.7936 (tttt) cc_final: 0.7715 (ttpp)
REVERT: A  457 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7747 (mm-30)
REVERT: B  407 VAL cc_start: 0.8799 (t) cc_final: 0.8464 (m)
REVERT: B  433 VAL cc_start: 0.7095 (m) cc_final: 0.6759 (p)
REVERT: B  449 TYR cc_start: 0.7464 (m-80) cc_final: 0.6803 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 170
  average time/residue: 0.5065
  time to fit residues: 91.0942
Evaluate side-chains
  172 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  427 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0470
   chunk 71 optimal weight:    0.9990
   chunk 66 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0050
   chunk 69 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0000
   chunk 22 optimal weight:    0.0970
   chunk 35 optimal weight:    0.0970
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.0492

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.166193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.145529 restraints weight = 27139.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 4.35
r_work: 0.3779 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3780
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3780 r_free = 0.3780    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.4153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6729  Z= 0.124
  Angle     :  0.674  14.258   9166  Z= 0.330
  Chirality :  0.043   0.172    979
  Planarity :  0.005   0.042   1172
  Dihedral  :  5.634  55.936   1026
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 22.16 %
    Favored  : 75.83 %
  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:  1.06 (0.30), residues: 790
  helix:  1.55 (0.26), residues: 399
  sheet:  0.37 (0.68), residues: 43
  loop : -0.18 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 192 
 TYR   0.021   0.002   TYR A 385 
 PHE   0.027   0.001   PHE B 377 
 TRP   0.017   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6712)
  covalent geometry    : angle       0.64467 ( 9128)
  SS BOND              : bond        0.00121 (    7)
  SS BOND              : angle       0.43279 (   14)
  hydrogen bonds       : bond        0.04131 (  318)
  hydrogen bonds       : angle       4.63637 (  925)
  metal coordination   : bond        0.00163 (    2)
  link_BETA1-4         : bond        0.01426 (    2)
  link_BETA1-4         : angle       6.53723 (    6)
  link_NAG-ASN         : bond        0.00307 (    6)
  link_NAG-ASN         : angle       2.44271 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7745 (mt-10)
REVERT: A  117 ASN cc_start: 0.8140 (m-40) cc_final: 0.7845 (m110)
REVERT: A  131 LYS cc_start: 0.7130 (pttm) cc_final: 0.6714 (pttm)
REVERT: A  281 LEU cc_start: 0.7726 (tt) cc_final: 0.7489 (mt)
REVERT: A  329 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7516 (tm-30)
REVERT: A  441 LYS cc_start: 0.7972 (tttt) cc_final: 0.7738 (ttpp)
REVERT: B  407 VAL cc_start: 0.8766 (t) cc_final: 0.8410 (m)
REVERT: B  433 VAL cc_start: 0.7043 (m) cc_final: 0.6745 (p)
  outliers start: 14
  outliers final: 4
  residues processed: 163
  average time/residue: 0.5255
  time to fit residues: 90.2092
Evaluate side-chains
  158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 LYS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  427 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0370
   chunk 29 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0980
   chunk 27 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0870
   chunk 43 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.0792

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 493 HIS
B 343 ASN
B 437 ASN
B 505 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.164421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.145253 restraints weight = 17508.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 3.13
r_work: 0.3845 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6729  Z= 0.126
  Angle     :  0.684  13.460   9166  Z= 0.336
  Chirality :  0.043   0.172    979
  Planarity :  0.005   0.039   1172
  Dihedral  :  5.613  56.660   1026
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 23.45 %
    Favored  : 73.81 %
  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:  1.11 (0.30), residues: 790
  helix:  1.59 (0.26), residues: 395
  sheet:  0.02 (0.65), residues: 43
  loop : -0.08 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 192 
 TYR   0.035   0.002   TYR A 183 
 PHE   0.029   0.001   PHE B 497 
 TRP   0.025   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6712)
  covalent geometry    : angle       0.65710 ( 9128)
  SS BOND              : bond        0.00127 (    7)
  SS BOND              : angle       0.40806 (   14)
  hydrogen bonds       : bond        0.04146 (  318)
  hydrogen bonds       : angle       4.59445 (  925)
  metal coordination   : bond        0.00169 (    2)
  link_BETA1-4         : bond        0.01321 (    2)
  link_BETA1-4         : angle       6.39361 (    6)
  link_NAG-ASN         : bond        0.00296 (    6)
  link_NAG-ASN         : angle       2.33075 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7871 (m-40) cc_final: 0.7552 (m-40)
REVERT: A   75 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7650 (mt-10)
REVERT: A  131 LYS cc_start: 0.7141 (pttm) cc_final: 0.6744 (pttm)
REVERT: A  215 TYR cc_start: 0.7822 (m-10) cc_final: 0.7533 (m-10)
REVERT: A  281 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7472 (mt)
REVERT: A  329 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: A  441 LYS cc_start: 0.7883 (tttt) cc_final: 0.7673 (ttpp)
REVERT: A  564 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7203 (tm-30)
REVERT: B  433 VAL cc_start: 0.6971 (m) cc_final: 0.6712 (p)
  outliers start: 19
  outliers final: 8
  residues processed: 173
  average time/residue: 0.5583
  time to fit residues: 101.6236
Evaluate side-chains
  166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain B residue  402 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0970
   chunk 77 optimal weight:    0.0060
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 56 optimal weight:    0.1980
   chunk 36 optimal weight:    0.4980
   chunk 33 optimal weight:    0.0670
   chunk 29 optimal weight:    0.1980
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.1132

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN
B 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.166186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.147705 restraints weight = 15088.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 2.90
r_work: 0.3867 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3870
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3870 r_free = 0.3870    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3870
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6729  Z= 0.131
  Angle     :  0.684  12.976   9166  Z= 0.337
  Chirality :  0.043   0.174    979
  Planarity :  0.004   0.037   1172
  Dihedral  :  5.632  56.782   1026
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 24.46 %
    Favored  : 73.53 %
  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:  1.01 (0.30), residues: 790
  helix:  1.55 (0.26), residues: 394
  sheet: -0.24 (0.66), residues: 44
  loop : -0.15 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 192 
 TYR   0.028   0.002   TYR A 183 
 PHE   0.034   0.002   PHE B 497 
 TRP   0.028   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6712)
  covalent geometry    : angle       0.65811 ( 9128)
  SS BOND              : bond        0.00135 (    7)
  SS BOND              : angle       0.38099 (   14)
  hydrogen bonds       : bond        0.04201 (  318)
  hydrogen bonds       : angle       4.52074 (  925)
  metal coordination   : bond        0.00232 (    2)
  link_BETA1-4         : bond        0.01248 (    2)
  link_BETA1-4         : angle       6.30797 (    6)
  link_NAG-ASN         : bond        0.00283 (    6)
  link_NAG-ASN         : angle       2.30376 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7595 (mt-10)
REVERT: A  215 TYR cc_start: 0.7810 (m-10) cc_final: 0.7514 (m-10)
REVERT: A  291 ILE cc_start: 0.7921 (mt) cc_final: 0.7692 (tp)
REVERT: A  329 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7396 (tm-30)
REVERT: A  474 MET cc_start: 0.6072 (mmm) cc_final: 0.5809 (mmm)
REVERT: A  489 GLU cc_start: 0.6723 (pm20) cc_final: 0.6446 (pp20)
REVERT: B  433 VAL cc_start: 0.6873 (m) cc_final: 0.6626 (p)
  outliers start: 14
  outliers final: 8
  residues processed: 167
  average time/residue: 0.5454
  time to fit residues: 96.0161
Evaluate side-chains
  167 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    0.0670
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0970
   chunk 35 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0370
   chunk 40 optimal weight:    0.0170
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.0570

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.167219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.146448 restraints weight = 23507.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 3.88
r_work: 0.3824 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3825 r_free = 0.3825    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3825 r_free = 0.3825    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6729  Z= 0.130
  Angle     :  0.705  12.607   9166  Z= 0.349
  Chirality :  0.043   0.171    979
  Planarity :  0.005   0.062   1172
  Dihedral  :  5.568  56.067   1026
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 25.47 %
    Favored  : 72.52 %
  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:  1.02 (0.30), residues: 790
  helix:  1.56 (0.26), residues: 395
  sheet: -0.10 (0.66), residues: 43
  loop : -0.18 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 192 
 TYR   0.022   0.002   TYR A 385 
 PHE   0.022   0.001   PHE B 377 
 TRP   0.033   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6712)
  covalent geometry    : angle       0.68053 ( 9128)
  SS BOND              : bond        0.00112 (    7)
  SS BOND              : angle       0.39028 (   14)
  hydrogen bonds       : bond        0.04189 (  318)
  hydrogen bonds       : angle       4.51991 (  925)
  metal coordination   : bond        0.00126 (    2)
  link_BETA1-4         : bond        0.01204 (    2)
  link_BETA1-4         : angle       6.21036 (    6)
  link_NAG-ASN         : bond        0.00311 (    6)
  link_NAG-ASN         : angle       2.24631 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 157
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7715 (mt-10)
REVERT: A  131 LYS cc_start: 0.7113 (pttm) cc_final: 0.6699 (pttm)
REVERT: A  291 ILE cc_start: 0.7947 (mt) cc_final: 0.7689 (tp)
REVERT: A  329 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: A  351 LEU cc_start: 0.7936 (mp) cc_final: 0.7734 (mp)
REVERT: A  474 MET cc_start: 0.6130 (mmm) cc_final: 0.5847 (mmm)
REVERT: A  489 GLU cc_start: 0.6803 (pm20) cc_final: 0.6391 (pp20)
REVERT: A  522 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8297 (pt0)
REVERT: B  433 VAL cc_start: 0.6933 (m) cc_final: 0.6671 (p)
REVERT: B  497 PHE cc_start: 0.7002 (m-10) cc_final: 0.6574 (m-10)
  outliers start: 14
  outliers final: 6
  residues processed: 167
  average time/residue: 0.5379
  time to fit residues: 94.8847
Evaluate side-chains
  162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain B residue  402 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0980
   chunk 60 optimal weight:    0.2980
   chunk 51 optimal weight:    0.2980
   chunk 53 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0970
   overall best weight:    0.1736

-------------------------------------------------------------------------------
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 = 0.4192 r_free = 0.4192 target = 0.164395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.146181 restraints weight = 13240.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 2.65
r_work: 0.3868 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3871
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3871 r_free = 0.3871    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3871 r_free = 0.3871    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.4876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6729  Z= 0.150
  Angle     :  0.734  12.132   9166  Z= 0.367
  Chirality :  0.044   0.209    979
  Planarity :  0.005   0.070   1172
  Dihedral  :  5.704  56.647   1026
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.32 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.30), residues: 790
  helix:  1.42 (0.26), residues: 401
  sheet: -0.05 (0.66), residues: 42
  loop : -0.26 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 192 
 TYR   0.027   0.002   TYR A  50 
 PHE   0.020   0.002   PHE B 377 
 TRP   0.047   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6712)
  covalent geometry    : angle       0.71145 ( 9128)
  SS BOND              : bond        0.00156 (    7)
  SS BOND              : angle       0.40631 (   14)
  hydrogen bonds       : bond        0.04440 (  318)
  hydrogen bonds       : angle       4.51823 (  925)
  metal coordination   : bond        0.00382 (    2)
  link_BETA1-4         : bond        0.01208 (    2)
  link_BETA1-4         : angle       6.07686 (    6)
  link_NAG-ASN         : bond        0.00293 (    6)
  link_NAG-ASN         : angle       2.24043 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7636 (mt-10)
REVERT: A  131 LYS cc_start: 0.7059 (pttm) cc_final: 0.6714 (pttm)
REVERT: A  329 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7433 (tm-30)
REVERT: A  351 LEU cc_start: 0.7860 (mp) cc_final: 0.7652 (mp)
REVERT: A  474 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5736 (mmp)
REVERT: A  522 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8230 (pt0)
REVERT: A  571 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6440 (tm-30)
REVERT: B  433 VAL cc_start: 0.7015 (m) cc_final: 0.6779 (p)
  outliers start: 18
  outliers final: 9
  residues processed: 172
  average time/residue: 0.5589
  time to fit residues: 101.1518
Evaluate side-chains
  172 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 160
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  474 MET
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.0370
   chunk 41 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0870
   chunk 59 optimal weight:    0.1980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.1434

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

Flipped N/Q/H residues before XYZ refinement:
B 343 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.164899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.144548 restraints weight = 20727.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 3.51
r_work: 0.3818 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3821
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3821 r_free = 0.3821    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.4970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6729  Z= 0.148
  Angle     :  0.747  11.537   9166  Z= 0.374
  Chirality :  0.044   0.176    979
  Planarity :  0.005   0.072   1172
  Dihedral  :  5.715  55.925   1026
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 26.47 %
    Favored  : 71.94 %
  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:  0.84 (0.30), residues: 790
  helix:  1.40 (0.26), residues: 399
  sheet: -0.07 (0.66), residues: 42
  loop : -0.28 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 192 
 TYR   0.028   0.002   TYR A  50 
 PHE   0.020   0.001   PHE B 377 
 TRP   0.041   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6712)
  covalent geometry    : angle       0.72589 ( 9128)
  SS BOND              : bond        0.00146 (    7)
  SS BOND              : angle       0.40905 (   14)
  hydrogen bonds       : bond        0.04423 (  318)
  hydrogen bonds       : angle       4.54658 (  925)
  metal coordination   : bond        0.00209 (    2)
  link_BETA1-4         : bond        0.01167 (    2)
  link_BETA1-4         : angle       6.00452 (    6)
  link_NAG-ASN         : bond        0.00266 (    6)
  link_NAG-ASN         : angle       2.26055 (   18)

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7616 (mt-10)
REVERT: A  131 LYS cc_start: 0.7046 (pttm) cc_final: 0.6682 (pttm)
REVERT: A  329 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: A  351 LEU cc_start: 0.7883 (mp) cc_final: 0.7682 (mp)
REVERT: A  489 GLU cc_start: 0.6821 (pm20) cc_final: 0.6368 (pp20)
REVERT: A  571 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6539 (tm-30)
REVERT: B  433 VAL cc_start: 0.7090 (m) cc_final: 0.6845 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 162
  average time/residue: 0.5661
  time to fit residues: 96.6924
Evaluate side-chains
  158 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue  402 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 37 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 20 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0770
   chunk 42 optimal weight:    0.2980
   chunk 45 optimal weight:    0.0970
   overall best weight:    0.1734

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

Flipped N/Q/H residues before XYZ refinement:
A 556 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.164561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.143506 restraints weight = 24654.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 3.90
r_work: 0.3792 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6729  Z= 0.153
  Angle     :  0.749  11.058   9166  Z= 0.375
  Chirality :  0.045   0.184    979
  Planarity :  0.005   0.071   1172
  Dihedral  :  5.787  55.828   1026
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 27.34 %
    Favored  : 71.37 %
  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:  0.70 (0.30), residues: 790
  helix:  1.25 (0.26), residues: 403
  sheet: -0.11 (0.66), residues: 42
  loop : -0.32 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 192 
 TYR   0.033   0.002   TYR A  50 
 PHE   0.018   0.002   PHE B 377 
 TRP   0.050   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6712)
  covalent geometry    : angle       0.72757 ( 9128)
  SS BOND              : bond        0.00146 (    7)
  SS BOND              : angle       0.41000 (   14)
  hydrogen bonds       : bond        0.04519 (  318)
  hydrogen bonds       : angle       4.55457 (  925)
  metal coordination   : bond        0.00295 (    2)
  link_BETA1-4         : bond        0.01208 (    2)
  link_BETA1-4         : angle       5.92985 (    6)
  link_NAG-ASN         : bond        0.00265 (    6)
  link_NAG-ASN         : angle       2.24213 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3267.75 seconds
wall clock time: 56 minutes 29.90 seconds (3389.90 seconds total)