Starting phenix.real_space_refine
on Mon Jun  9 14:35:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv0_38688/06_2025/8xv0_38688.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.034
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 4904 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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4241      2.51       5
     N    1078      2.21       5
     O    1277      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6633
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 1559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1559
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 12, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      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: "F"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.45, per 1000 atoms: 0.82
  Number of scatterers: 6633
  At special positions: 0
  Unit cell: (87.435, 86.43, 118.59, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1277      8.00
     N    1078      7.00
     C    4241      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 524 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 487 " 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
    ALPHA1-3
      " BMA F   3 " - " MAN F   4 "
    ALPHA1-6
      " BMA F   3 " - " MAN F   5 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A 322 "
      " NAG A 702 " - " ASN A 432 "
      " NAG B1300 " - " ASN B 343 "
      " NAG B1301 " - " ASN B 354 "
      " NAG C   1 " - " ASN A  53 "
      " NAG D   1 " - " ASN A 546 "
      " NAG E   1 " - " ASN A  90 "
      " NAG F   1 " - " ASN A 103 "
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      55.9% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.520A  pdb=" N   PHE A  28 " --> pdb=" O   GLN A  24 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 80
    Processing helix  chain 'A' and resid 81 through 83
      No H-bonds generated for 'chain 'A' and resid 81 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.968A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 92 through 105
    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 174
    Processing helix  chain 'A' and resid 176 through 194
    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: 4.117A  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 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    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: 3.876A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.501A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.782A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   HIS A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.569A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 412
      removed outlier: 4.045A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.711A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.345A  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 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.719A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 559
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
      removed outlier: 3.511A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.515A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 4.092A  pdb=" N   VAL B 367 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 368 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 3.651A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.105A  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 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.686A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 515 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLU B 515 " --> pdb=" O   ASN B 394 " (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

    307 hydrogen bonds defined for protein.
    879 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: 1.92

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2083
        1.34 -     1.46: 1770
        1.46 -     1.58: 2910
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6821
  Sorted by residual:
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.39e+00
  bond pdb=" C1  BMA F   3 "
       pdb=" C2  BMA F   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.550 -0.031 2.00e-02 2.50e+03 2.37e+00
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" C1  MAN F   4 "
       pdb=" C2  MAN F   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.554 -0.028 2.00e-02 2.50e+03 1.90e+00
  ... (remaining 6816 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 8956
        1.28 -     2.56: 225
        2.56 -     3.84: 57
        3.84 -     5.12: 26
        5.12 -     6.39: 7
  Bond angle restraints: 9271
  Sorted by residual:
  angle pdb=" C   PRO A 135 "
        pdb=" N   ASP A 136 "
        pdb=" CA  ASP A 136 "
      ideal   model   delta    sigma   weight residual
     121.54  125.96   -4.42 1.91e+00 2.74e-01 5.36e+00
  angle pdb=" CA  ASP A 136 "
        pdb=" CB  ASP A 136 "
        pdb=" CG  ASP A 136 "
      ideal   model   delta    sigma   weight residual
     112.60  114.88   -2.28 1.00e+00 1.00e+00 5.20e+00
  angle pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
        pdb=" SG  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     114.40  119.39   -4.99 2.30e+00 1.89e-01 4.70e+00
  angle pdb=" C3  BMA F   3 "
        pdb=" C2  BMA F   3 "
        pdb=" O2  BMA F   3 "
      ideal   model   delta    sigma   weight residual
     112.95  106.56    6.39 3.00e+00 1.11e-01 4.54e+00
  angle pdb=" C3  MAN F   5 "
        pdb=" C2  MAN F   5 "
        pdb=" O2  MAN F   5 "
      ideal   model   delta    sigma   weight residual
     111.77  105.39    6.38 3.00e+00 1.11e-01 4.52e+00
  ... (remaining 9266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.00: 3964
       22.00 -    44.00: 220
       44.00 -    66.00: 15
       66.00 -    88.01: 16
       88.01 -   110.01: 9
  Dihedral angle restraints: 4224
    sinusoidal: 1903
      harmonic: 2321
  Sorted by residual:
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 524 "
           pdb=" CB  CYS B 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    8.76   84.24     1      1.00e+01 1.00e-02 8.64e+01
  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 -129.66   43.66     1      1.00e+01 1.00e-02 2.66e+01
  dihedral pdb=" O4  BMA E   3 "
           pdb=" C4  BMA E   3 "
           pdb=" C5  BMA E   3 "
           pdb=" O5  BMA E   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  178.70  110.01     1      3.00e+01 1.11e-03 1.43e+01
  ... (remaining 4221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 1008
       0.142 -    0.284: 4
       0.284 -    0.426: 1
       0.426 -    0.569: 0
       0.569 -    0.711: 1
  Chirality restraints: 1014
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.69   -0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" C5  BMA F   3 "
            pdb=" C4  BMA F   3 "
            pdb=" C6  BMA F   3 "
            pdb=" O5  BMA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.84e+00
  ... (remaining 1011 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 103 "   -0.018 2.00e-02 2.50e+03   1.73e-02 3.75e+00
        pdb=" CG  ASN A 103 "    0.015 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 103 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 103 "    0.023 2.00e-02 2.50e+03
        pdb=" C1  NAG F   1 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 226 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   VAL A 226 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   VAL A 226 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLU A 227 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 241 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.59e+00
        pdb=" C   HIS A 241 "    0.028 2.00e-02 2.50e+03
        pdb=" O   HIS A 241 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 242 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1320
        2.77 -     3.31: 6166
        3.31 -     3.84: 10591
        3.84 -     4.37: 11686
        4.37 -     4.90: 20940
  Nonbonded interactions: 50703
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 563 "
            pdb=" OE1 GLU A 564 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER A 611 "
            pdb=" O   ALA A 614 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" OD2 ASP B 467 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   MET A 152 "
            pdb=" NH1 ARG A 161 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" NH1 ARG A 177 "
            pdb=" O   GLU A 495 "
     model   vdw
     2.318 3.120
  ... (remaining 50698 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     20.420
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:13.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6140
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6844  Z= 0.160
  Angle     :  0.600   8.265   9333  Z= 0.283
  Chirality :  0.049   0.711   1014
  Planarity :  0.003   0.025   1175
  Dihedral  : 14.697 110.007   2713
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.31), residues: 786
  helix:  1.87 (0.28), residues: 395
  sheet:  1.62 (0.81), residues: 44
  loop : -0.71 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 203 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.010   0.001   PHE B 347 
 TYR   0.023   0.001   TYR A 199 
 ARG   0.003   0.000   ARG A 204 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00712 (    8)
  link_NAG-ASN         : angle       3.60831 (   24)
  link_ALPHA1-6        : bond        0.00409 (    1)
  link_ALPHA1-6        : angle       1.60825 (    3)
  link_BETA1-4         : bond        0.00327 (    6)
  link_BETA1-4         : angle       1.95543 (   18)
  link_ALPHA1-3        : bond        0.00401 (    1)
  link_ALPHA1-3        : angle       1.47651 (    3)
  hydrogen bonds       : bond        0.15650 (  307)
  hydrogen bonds       : angle       6.12422 (  879)
  SS BOND              : bond        0.00119 (    7)
  SS BOND              : angle       1.76926 (   14)
  covalent geometry    : bond        0.00320 ( 6821)
  covalent geometry    : angle       0.56093 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A   37 GLU cc_start: 0.6388 (mt-10) cc_final: 0.5950 (mt-10)
REVERT: A   81 GLN cc_start: 0.7959 (mt0) cc_final: 0.7191 (mm110)
REVERT: A  182 GLU cc_start: 0.6543 (tt0) cc_final: 0.6203 (mp0)
REVERT: A  190 MET cc_start: 0.5700 (tmm) cc_final: 0.5209 (tmm)
REVERT: A  231 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6280 (mt-10)
REVERT: A  295 ASP cc_start: 0.5526 (m-30) cc_final: 0.5216 (m-30)
REVERT: A  441 LYS cc_start: 0.6526 (tttt) cc_final: 0.6256 (ttpp)
REVERT: A  546 ASN cc_start: 0.6704 (m110) cc_final: 0.5429 (p0)
REVERT: A  579 MET cc_start: 0.7122 (mtm) cc_final: 0.6827 (mtm)
REVERT: A  585 LEU cc_start: 0.6637 (mt) cc_final: 0.6425 (mm)
REVERT: B  357 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6958 (ttt-90)
REVERT: B  378 LYS cc_start: 0.6314 (mmtt) cc_final: 0.5556 (tptp)
REVERT: B  394 ASN cc_start: 0.6702 (m110) cc_final: 0.6289 (m110)
REVERT: B  440 LYS cc_start: 0.7498 (tmtt) cc_final: 0.7255 (mptt)
REVERT: B  462 LYS cc_start: 0.7046 (mmtp) cc_final: 0.6711 (mppt)
REVERT: B  468 ILE cc_start: 0.8069 (mt) cc_final: 0.7848 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 1.2609
  time to fit residues: 198.1870
Evaluate side-chains
  90 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 39 optimal weight:    0.0370
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS
A 121 ASN
A 210 ASN
A 531 GLN
B 388 ASN
B 486 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.166531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.134697 restraints weight = 7848.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.04
r_work: 0.3359 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6844  Z= 0.137
  Angle     :  0.619  10.726   9333  Z= 0.301
  Chirality :  0.044   0.319   1014
  Planarity :  0.004   0.032   1175
  Dihedral  : 10.687  78.288   1185
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 10.37 %
    Favored  : 87.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.31), residues: 786
  helix:  2.00 (0.27), residues: 405
  sheet:  1.53 (0.81), residues: 42
  loop : -0.68 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 535 
 PHE   0.016   0.001   PHE B 347 
 TYR   0.015   0.001   TYR A 199 
 ARG   0.005   0.001   ARG B 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01139 (    8)
  link_NAG-ASN         : angle       4.35136 (   24)
  link_ALPHA1-6        : bond        0.00339 (    1)
  link_ALPHA1-6        : angle       1.76335 (    3)
  link_BETA1-4         : bond        0.00364 (    6)
  link_BETA1-4         : angle       2.12925 (   18)
  link_ALPHA1-3        : bond        0.01324 (    1)
  link_ALPHA1-3        : angle       2.08040 (    3)
  hydrogen bonds       : bond        0.05443 (  307)
  hydrogen bonds       : angle       4.34878 (  879)
  SS BOND              : bond        0.00171 (    7)
  SS BOND              : angle       1.70486 (   14)
  covalent geometry    : bond        0.00286 ( 6821)
  covalent geometry    : angle       0.56712 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7345 (mt-10)
REVERT: A   81 GLN cc_start: 0.8152 (mt0) cc_final: 0.7814 (mm110)
REVERT: A  131 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7210 (ttmt)
REVERT: A  190 MET cc_start: 0.7147 (tmm) cc_final: 0.6531 (tmm)
REVERT: A  295 ASP cc_start: 0.7140 (m-30) cc_final: 0.6795 (m-30)
REVERT: A  376 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8196 (mmt)
REVERT: A  527 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7280 (tt0)
REVERT: A  546 ASN cc_start: 0.7410 (m110) cc_final: 0.6402 (p0)
REVERT: A  579 MET cc_start: 0.7843 (mtm) cc_final: 0.7426 (mtm)
REVERT: B  378 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7227 (tptp)
  outliers start: 17
  outliers final: 8
  residues processed: 106
  average time/residue: 1.2165
  time to fit residues: 135.6380
Evaluate side-chains
  94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 MET
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B 388 ASN
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.162445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.130835 restraints weight = 7909.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.06
r_work: 0.3258 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6844  Z= 0.184
  Angle     :  0.673  10.456   9333  Z= 0.335
  Chirality :  0.048   0.355   1014
  Planarity :  0.004   0.050   1175
  Dihedral  :  9.404  74.651   1185
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.54 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.31), residues: 786
  helix:  1.80 (0.27), residues: 400
  sheet:  0.65 (0.71), residues: 52
  loop : -0.75 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.026   0.002   PHE B 347 
 TYR   0.022   0.002   TYR A 385 
 ARG   0.003   0.001   ARG B 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00657 (    8)
  link_NAG-ASN         : angle       3.63708 (   24)
  link_ALPHA1-6        : bond        0.00341 (    1)
  link_ALPHA1-6        : angle       1.46786 (    3)
  link_BETA1-4         : bond        0.00451 (    6)
  link_BETA1-4         : angle       2.53469 (   18)
  link_ALPHA1-3        : bond        0.01477 (    1)
  link_ALPHA1-3        : angle       1.50546 (    3)
  hydrogen bonds       : bond        0.06873 (  307)
  hydrogen bonds       : angle       4.30457 (  879)
  SS BOND              : bond        0.00259 (    7)
  SS BOND              : angle       2.12139 (   14)
  covalent geometry    : bond        0.00425 ( 6821)
  covalent geometry    : angle       0.63360 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: A   81 GLN cc_start: 0.8329 (mt0) cc_final: 0.7993 (mm110)
REVERT: A  131 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7333 (ttmt)
REVERT: A  190 MET cc_start: 0.7269 (tmm) cc_final: 0.6412 (tmm)
REVERT: A  295 ASP cc_start: 0.7181 (m-30) cc_final: 0.6786 (m-30)
REVERT: A  401 HIS cc_start: 0.8278 (OUTLIER) cc_final: 0.7790 (m-70)
REVERT: A  527 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7487 (tt0)
REVERT: B  378 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7370 (tptp)
REVERT: B  462 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7625 (mttm)
  outliers start: 19
  outliers final: 10
  residues processed: 95
  average time/residue: 1.2694
  time to fit residues: 128.3633
Evaluate side-chains
  92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.162822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.130229 restraints weight = 7903.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.19
r_work: 0.3268 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6844  Z= 0.130
  Angle     :  0.598   9.471   9333  Z= 0.292
  Chirality :  0.044   0.342   1014
  Planarity :  0.003   0.028   1175
  Dihedral  :  8.512  73.642   1185
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.12 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.31), residues: 786
  helix:  2.05 (0.27), residues: 391
  sheet:  0.78 (0.70), residues: 52
  loop : -0.83 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.010   0.001   PHE B 342 
 TYR   0.013   0.001   TYR A 385 
 ARG   0.002   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00765 (    8)
  link_NAG-ASN         : angle       3.45517 (   24)
  link_ALPHA1-6        : bond        0.00469 (    1)
  link_ALPHA1-6        : angle       1.57755 (    3)
  link_BETA1-4         : bond        0.00453 (    6)
  link_BETA1-4         : angle       2.41656 (   18)
  link_ALPHA1-3        : bond        0.01342 (    1)
  link_ALPHA1-3        : angle       1.79177 (    3)
  hydrogen bonds       : bond        0.05638 (  307)
  hydrogen bonds       : angle       4.22232 (  879)
  SS BOND              : bond        0.00134 (    7)
  SS BOND              : angle       1.74762 (   14)
  covalent geometry    : bond        0.00273 ( 6821)
  covalent geometry    : angle       0.55767 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7556 (mt-10)
REVERT: A   81 GLN cc_start: 0.8382 (mt0) cc_final: 0.8002 (mm110)
REVERT: A  131 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7258 (ttmt)
REVERT: A  156 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7318 (tt)
REVERT: A  190 MET cc_start: 0.7174 (tmm) cc_final: 0.6326 (tmm)
REVERT: A  295 ASP cc_start: 0.7093 (m-30) cc_final: 0.6723 (m-30)
REVERT: A  401 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7606 (m-70)
REVERT: A  527 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7364 (tt0)
REVERT: A  546 ASN cc_start: 0.7468 (m110) cc_final: 0.6431 (p0)
REVERT: A  579 MET cc_start: 0.7875 (mtm) cc_final: 0.7542 (mtm)
REVERT: A  600 LYS cc_start: 0.7744 (pttm) cc_final: 0.7428 (pttt)
REVERT: B  378 LYS cc_start: 0.7471 (mmtt) cc_final: 0.7215 (tptp)
REVERT: B  417 ASN cc_start: 0.7909 (t160) cc_final: 0.7657 (t0)
REVERT: B  440 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8183 (mptt)
REVERT: B  462 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7494 (mtpt)
  outliers start: 25
  outliers final: 11
  residues processed: 99
  average time/residue: 1.4440
  time to fit residues: 152.1376
Evaluate side-chains
  94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0270
   chunk 52 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 287 GLN
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.163737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.132198 restraints weight = 7831.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.19
r_work: 0.3292 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6844  Z= 0.119
  Angle     :  0.559   9.007   9333  Z= 0.275
  Chirality :  0.043   0.335   1014
  Planarity :  0.003   0.029   1175
  Dihedral  :  7.526  70.219   1185
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.84 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.31), residues: 786
  helix:  2.13 (0.27), residues: 392
  sheet:  0.81 (0.70), residues: 52
  loop : -0.80 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.009   0.001   PHE B 347 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00661 (    8)
  link_NAG-ASN         : angle       3.25683 (   24)
  link_ALPHA1-6        : bond        0.00687 (    1)
  link_ALPHA1-6        : angle       1.57256 (    3)
  link_BETA1-4         : bond        0.00443 (    6)
  link_BETA1-4         : angle       2.10552 (   18)
  link_ALPHA1-3        : bond        0.01251 (    1)
  link_ALPHA1-3        : angle       1.76944 (    3)
  hydrogen bonds       : bond        0.05138 (  307)
  hydrogen bonds       : angle       4.15222 (  879)
  SS BOND              : bond        0.00149 (    7)
  SS BOND              : angle       1.70280 (   14)
  covalent geometry    : bond        0.00248 ( 6821)
  covalent geometry    : angle       0.52169 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 86
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7378 (mt-10)
REVERT: A   81 GLN cc_start: 0.8498 (mt0) cc_final: 0.8134 (mm110)
REVERT: A  131 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7234 (ttmt)
REVERT: A  190 MET cc_start: 0.7125 (tmm) cc_final: 0.6302 (tmm)
REVERT: A  224 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7034 (mm-30)
REVERT: A  295 ASP cc_start: 0.7103 (m-30) cc_final: 0.6741 (m-30)
REVERT: A  383 MET cc_start: 0.8610 (mtp) cc_final: 0.8188 (mtm)
REVERT: A  401 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7528 (m-70)
REVERT: A  546 ASN cc_start: 0.7180 (m110) cc_final: 0.6256 (p0)
REVERT: A  571 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7994 (tt0)
REVERT: A  579 MET cc_start: 0.7743 (mtm) cc_final: 0.7466 (mtm)
REVERT: B  378 LYS cc_start: 0.7429 (mmtt) cc_final: 0.7141 (tptp)
REVERT: B  417 ASN cc_start: 0.7894 (t160) cc_final: 0.7641 (t0)
REVERT: B  462 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7397 (mtpt)
  outliers start: 24
  outliers final: 10
  residues processed: 102
  average time/residue: 1.4106
  time to fit residues: 154.3066
Evaluate side-chains
  95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 287 GLN
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.163094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.131160 restraints weight = 7799.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.10
r_work: 0.3278 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6844  Z= 0.132
  Angle     :  0.580   8.898   9333  Z= 0.286
  Chirality :  0.044   0.319   1014
  Planarity :  0.003   0.028   1175
  Dihedral  :  7.289  68.083   1185
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.99 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.31), residues: 786
  helix:  2.06 (0.27), residues: 394
  sheet:  0.80 (0.70), residues: 52
  loop : -0.85 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.010   0.001   PHE B 342 
 TYR   0.014   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00602 (    8)
  link_NAG-ASN         : angle       3.23203 (   24)
  link_ALPHA1-6        : bond        0.00676 (    1)
  link_ALPHA1-6        : angle       1.48925 (    3)
  link_BETA1-4         : bond        0.00440 (    6)
  link_BETA1-4         : angle       2.03466 (   18)
  link_ALPHA1-3        : bond        0.01293 (    1)
  link_ALPHA1-3        : angle       1.80840 (    3)
  hydrogen bonds       : bond        0.05475 (  307)
  hydrogen bonds       : angle       4.17099 (  879)
  SS BOND              : bond        0.00128 (    7)
  SS BOND              : angle       1.67161 (   14)
  covalent geometry    : bond        0.00289 ( 6821)
  covalent geometry    : angle       0.54591 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7393 (mt-10)
REVERT: A   81 GLN cc_start: 0.8504 (mt0) cc_final: 0.8163 (mm110)
REVERT: A  131 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7246 (ttmt)
REVERT: A  156 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7309 (tt)
REVERT: A  190 MET cc_start: 0.7159 (tmm) cc_final: 0.6325 (tmm)
REVERT: A  224 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7025 (mm-30)
REVERT: A  295 ASP cc_start: 0.7099 (m-30) cc_final: 0.6738 (m-30)
REVERT: A  383 MET cc_start: 0.8621 (mtp) cc_final: 0.8222 (mtm)
REVERT: A  546 ASN cc_start: 0.7189 (m110) cc_final: 0.6230 (p0)
REVERT: A  579 MET cc_start: 0.7815 (mtm) cc_final: 0.7504 (mtm)
REVERT: B  378 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7221 (tmtt)
REVERT: B  417 ASN cc_start: 0.7899 (t160) cc_final: 0.7656 (t0)
REVERT: B  440 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8185 (mptt)
REVERT: B  462 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7441 (mtpt)
  outliers start: 22
  outliers final: 12
  residues processed: 96
  average time/residue: 1.2363
  time to fit residues: 125.6845
Evaluate side-chains
  96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   chunk 59 optimal weight:    0.3980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.163293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.130868 restraints weight = 7838.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 2.06
r_work: 0.3289 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6844  Z= 0.126
  Angle     :  0.566   8.741   9333  Z= 0.280
  Chirality :  0.044   0.327   1014
  Planarity :  0.003   0.030   1175
  Dihedral  :  7.060  65.491   1185
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.71 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.31), residues: 786
  helix:  2.07 (0.27), residues: 395
  sheet:  0.82 (0.69), residues: 52
  loop : -0.81 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.011   0.001   PHE B 371 
 TYR   0.013   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00563 (    8)
  link_NAG-ASN         : angle       3.16716 (   24)
  link_ALPHA1-6        : bond        0.00742 (    1)
  link_ALPHA1-6        : angle       1.45494 (    3)
  link_BETA1-4         : bond        0.00434 (    6)
  link_BETA1-4         : angle       1.93984 (   18)
  link_ALPHA1-3        : bond        0.01253 (    1)
  link_ALPHA1-3        : angle       1.79423 (    3)
  hydrogen bonds       : bond        0.05305 (  307)
  hydrogen bonds       : angle       4.15481 (  879)
  SS BOND              : bond        0.00118 (    7)
  SS BOND              : angle       1.61825 (   14)
  covalent geometry    : bond        0.00272 ( 6821)
  covalent geometry    : angle       0.53247 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: A   81 GLN cc_start: 0.8501 (mt0) cc_final: 0.8173 (mm110)
REVERT: A  131 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7186 (ttmt)
REVERT: A  190 MET cc_start: 0.7149 (tmm) cc_final: 0.6317 (tmm)
REVERT: A  224 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7044 (mm-30)
REVERT: A  295 ASP cc_start: 0.7153 (m-30) cc_final: 0.6817 (m-30)
REVERT: A  383 MET cc_start: 0.8638 (mtp) cc_final: 0.8234 (mtm)
REVERT: A  401 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7814 (m-70)
REVERT: A  527 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7227 (tt0)
REVERT: A  546 ASN cc_start: 0.7177 (m110) cc_final: 0.6224 (p0)
REVERT: A  571 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7959 (tt0)
REVERT: A  579 MET cc_start: 0.7784 (mtm) cc_final: 0.7466 (mtm)
REVERT: B  417 ASN cc_start: 0.7873 (t160) cc_final: 0.7632 (t0)
REVERT: B  462 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7438 (mtpt)
  outliers start: 21
  outliers final: 12
  residues processed: 96
  average time/residue: 1.1735
  time to fit residues: 119.1972
Evaluate side-chains
  96 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0020
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.163818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.131815 restraints weight = 7876.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.15
r_work: 0.3264 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6844  Z= 0.122
  Angle     :  0.565   8.413   9333  Z= 0.278
  Chirality :  0.043   0.317   1014
  Planarity :  0.003   0.027   1175
  Dihedral  :  6.841  62.398   1185
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.99 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.31), residues: 786
  helix:  2.03 (0.27), residues: 397
  sheet:  0.85 (0.69), residues: 52
  loop : -0.78 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.010   0.001   PHE B 371 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00554 (    8)
  link_NAG-ASN         : angle       3.07453 (   24)
  link_ALPHA1-6        : bond        0.00788 (    1)
  link_ALPHA1-6        : angle       1.45327 (    3)
  link_BETA1-4         : bond        0.00449 (    6)
  link_BETA1-4         : angle       1.86724 (   18)
  link_ALPHA1-3        : bond        0.01270 (    1)
  link_ALPHA1-3        : angle       1.83170 (    3)
  hydrogen bonds       : bond        0.05203 (  307)
  hydrogen bonds       : angle       4.16212 (  879)
  SS BOND              : bond        0.00097 (    7)
  SS BOND              : angle       1.54357 (   14)
  covalent geometry    : bond        0.00262 ( 6821)
  covalent geometry    : angle       0.53321 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7376 (mt-10)
REVERT: A   81 GLN cc_start: 0.8509 (mt0) cc_final: 0.8176 (mm-40)
REVERT: A  131 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7152 (ttmt)
REVERT: A  156 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7215 (tt)
REVERT: A  190 MET cc_start: 0.7166 (tmm) cc_final: 0.6322 (tmm)
REVERT: A  224 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7057 (mm-30)
REVERT: A  295 ASP cc_start: 0.7229 (m-30) cc_final: 0.6882 (m-30)
REVERT: A  383 MET cc_start: 0.8640 (mtp) cc_final: 0.8242 (mtm)
REVERT: A  401 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7820 (m-70)
REVERT: A  546 ASN cc_start: 0.7151 (m110) cc_final: 0.6202 (p0)
REVERT: A  571 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7961 (tt0)
REVERT: A  579 MET cc_start: 0.7774 (mtm) cc_final: 0.7440 (mtm)
REVERT: B  417 ASN cc_start: 0.7874 (t160) cc_final: 0.7647 (t0)
REVERT: B  440 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8116 (mmtm)
REVERT: B  462 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7430 (mtpt)
  outliers start: 21
  outliers final: 13
  residues processed: 95
  average time/residue: 1.0648
  time to fit residues: 107.3357
Evaluate side-chains
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 63 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0770
   chunk 11 optimal weight:    8.9990
   chunk 72 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6340

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.163886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.131505 restraints weight = 7899.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.09
r_work: 0.3287 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6844  Z= 0.121
  Angle     :  0.561   8.113   9333  Z= 0.277
  Chirality :  0.043   0.301   1014
  Planarity :  0.003   0.028   1175
  Dihedral  :  6.707  60.410   1185
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.43 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.31), residues: 786
  helix:  1.98 (0.27), residues: 397
  sheet:  0.89 (0.69), residues: 52
  loop : -0.80 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 540 
 PHE   0.009   0.001   PHE B 342 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (    8)
  link_NAG-ASN         : angle       3.02570 (   24)
  link_ALPHA1-6        : bond        0.00808 (    1)
  link_ALPHA1-6        : angle       1.42935 (    3)
  link_BETA1-4         : bond        0.00458 (    6)
  link_BETA1-4         : angle       1.83656 (   18)
  link_ALPHA1-3        : bond        0.01280 (    1)
  link_ALPHA1-3        : angle       1.84356 (    3)
  hydrogen bonds       : bond        0.05167 (  307)
  hydrogen bonds       : angle       4.16222 (  879)
  SS BOND              : bond        0.00094 (    7)
  SS BOND              : angle       1.58046 (   14)
  covalent geometry    : bond        0.00258 ( 6821)
  covalent geometry    : angle       0.53008 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: A   81 GLN cc_start: 0.8526 (mt0) cc_final: 0.8184 (mm110)
REVERT: A  131 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7155 (ttmt)
REVERT: A  156 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7203 (tt)
REVERT: A  190 MET cc_start: 0.7161 (tmm) cc_final: 0.6317 (tmm)
REVERT: A  224 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7059 (mm-30)
REVERT: A  295 ASP cc_start: 0.7192 (m-30) cc_final: 0.6841 (m-30)
REVERT: A  383 MET cc_start: 0.8629 (mtp) cc_final: 0.8234 (mtm)
REVERT: A  401 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7804 (m-70)
REVERT: A  527 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7239 (tt0)
REVERT: A  546 ASN cc_start: 0.7171 (m110) cc_final: 0.6241 (p0)
REVERT: A  571 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7941 (tt0)
REVERT: A  579 MET cc_start: 0.7741 (mtm) cc_final: 0.7411 (mtm)
REVERT: B  417 ASN cc_start: 0.7865 (t160) cc_final: 0.7635 (t0)
REVERT: B  440 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8112 (mmtm)
REVERT: B  462 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7428 (mtpt)
  outliers start: 21
  outliers final: 13
  residues processed: 97
  average time/residue: 1.0779
  time to fit residues: 110.9905
Evaluate side-chains
  99 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain A residue  571 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 72 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0010
   chunk 59 optimal weight:    0.0070
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.4804

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.164937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.132283 restraints weight = 7938.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.12
r_work: 0.3281 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6844  Z= 0.111
  Angle     :  0.548   7.753   9333  Z= 0.270
  Chirality :  0.043   0.298   1014
  Planarity :  0.003   0.028   1175
  Dihedral  :  6.441  56.599   1185
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 17.87 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.31), residues: 786
  helix:  2.07 (0.27), residues: 397
  sheet:  0.93 (0.69), residues: 52
  loop : -0.77 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 378 
 PHE   0.008   0.001   PHE A 315 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 482 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00529 (    8)
  link_NAG-ASN         : angle       2.91475 (   24)
  link_ALPHA1-6        : bond        0.00863 (    1)
  link_ALPHA1-6        : angle       1.44049 (    3)
  link_BETA1-4         : bond        0.00462 (    6)
  link_BETA1-4         : angle       1.73184 (   18)
  link_ALPHA1-3        : bond        0.01226 (    1)
  link_ALPHA1-3        : angle       1.84328 (    3)
  hydrogen bonds       : bond        0.04806 (  307)
  hydrogen bonds       : angle       4.15032 (  879)
  SS BOND              : bond        0.00084 (    7)
  SS BOND              : angle       1.50981 (   14)
  covalent geometry    : bond        0.00229 ( 6821)
  covalent geometry    : angle       0.51853 ( 9271)

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7334 (mt-10)
REVERT: A   81 GLN cc_start: 0.8498 (mt0) cc_final: 0.8197 (mm-40)
REVERT: A  131 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7161 (ttmt)
REVERT: A  156 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7166 (tt)
REVERT: A  190 MET cc_start: 0.7156 (tmm) cc_final: 0.6328 (tmm)
REVERT: A  224 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6998 (mm-30)
REVERT: A  295 ASP cc_start: 0.7193 (m-30) cc_final: 0.6837 (m-30)
REVERT: A  383 MET cc_start: 0.8618 (mtp) cc_final: 0.8231 (mtm)
REVERT: A  401 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7808 (m-70)
REVERT: A  527 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7245 (tt0)
REVERT: A  546 ASN cc_start: 0.7093 (m110) cc_final: 0.6157 (p0)
REVERT: A  579 MET cc_start: 0.7647 (mtm) cc_final: 0.7317 (mtm)
REVERT: B  388 ASN cc_start: 0.7255 (m-40) cc_final: 0.6927 (t0)
REVERT: B  440 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8102 (mmtm)
REVERT: B  462 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7393 (mtpt)
  outliers start: 16
  outliers final: 9
  residues processed: 90
  average time/residue: 1.2406
  time to fit residues: 119.3491
Evaluate side-chains
  93 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  131 LYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  224 GLU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  527 GLU
Chi-restraints excluded: chain A residue  543 ASP
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  462 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0050
   chunk 41 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.165268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.133123 restraints weight = 7880.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.09
r_work: 0.3280 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6844  Z= 0.112
  Angle     :  0.545   7.472   9333  Z= 0.269
  Chirality :  0.043   0.298   1014
  Planarity :  0.003   0.028   1175
  Dihedral  :  6.129  50.780   1185
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.58 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.31), residues: 786
  helix:  2.12 (0.27), residues: 397
  sheet:  0.93 (0.69), residues: 52
  loop : -0.77 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.002   0.001   HIS A 540 
 PHE   0.008   0.001   PHE A 327 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00518 (    8)
  link_NAG-ASN         : angle       2.82427 (   24)
  link_ALPHA1-6        : bond        0.00885 (    1)
  link_ALPHA1-6        : angle       1.33943 (    3)
  link_BETA1-4         : bond        0.00461 (    6)
  link_BETA1-4         : angle       1.66636 (   18)
  link_ALPHA1-3        : bond        0.01237 (    1)
  link_ALPHA1-3        : angle       1.88755 (    3)
  hydrogen bonds       : bond        0.04735 (  307)
  hydrogen bonds       : angle       4.12171 (  879)
  SS BOND              : bond        0.00084 (    7)
  SS BOND              : angle       1.47171 (   14)
  covalent geometry    : bond        0.00231 ( 6821)
  covalent geometry    : angle       0.51717 ( 9271)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5592.26 seconds
wall clock time: 98 minutes 45.04 seconds (5925.04 seconds total)