Starting phenix.real_space_refine
on Tue Jun 10 11:29:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wdz_37468/06_2025/8wdz_37468.cif"
  }
  resolution = 2.71
  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=   0.001 sd=   0.026
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 6336 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4195      2.51       5
     N    1078      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 6559
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1553
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    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: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 57
          Unusual residues: {' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.11, per 1000 atoms: 1.08
  Number of scatterers: 6559
  At special positions: 0
  Unit cell: (76.5, 87.55, 124.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1248      8.00
     N    1078      7.00
     C    4195      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=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 901 " - " ASN A  53 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 322 "
      " NAG A 904 " - " ASN A 432 "
      " NAG B 601 " - " ASN B 343 "
      " NAG C   1 " - " ASN A 103 "
      " NAG D   1 " - " ASN A 546 "
  Time building additional restraints: 1.99
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 905 "
        pdb="ZN    ZN A 905 " - pdb=" NE2 HIS A 378 "
        pdb="ZN    ZN A 905 " - pdb=" NE2 HIS A 374 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      54.5% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.528A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR A  27 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 4.346A  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: 3.667A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 101
      removed outlier: 3.783A  pdb=" N   GLN A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.949A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 147 through 154
    Processing helix  chain 'A' and resid 157 through 172
      removed outlier: 3.762A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG A 169 " --> pdb=" O   TRP A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 194
      removed outlier: 3.895A  pdb=" N   LEU A 176 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.687A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    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 249
      removed outlier: 3.716A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A 232 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.727A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.757A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.624A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 400 through 411
      removed outlier: 3.860A  pdb=" N   VAL A 404 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.839A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 436 " --> pdb=" O   ASN A 432 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   THR A 445 " --> pdb=" O   LYS A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 466
    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: 4.083A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.922A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.798A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
      removed outlier: 3.530A  pdb=" N   PHE A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 5.024A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.443A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352
      removed outlier: 6.066A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 4.181A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   CYS B 432 " --> pdb=" O   LEU B 513 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474

    290 hydrogen bonds defined for protein.
    821 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: 1.71

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2082
        1.34 -     1.46: 1737
        1.46 -     1.58: 2867
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6744
  Sorted by residual:
  bond pdb=" CA  SER B 494 "
       pdb=" CB  SER B 494 "
    ideal  model  delta    sigma   weight residual
    1.530  1.478  0.052 1.43e-02 4.89e+03 1.32e+01
  bond pdb=" CE1 HIS A 401 "
       pdb=" NE2 HIS A 401 "
    ideal  model  delta    sigma   weight residual
    1.321  1.355 -0.034 1.00e-02 1.00e+04 1.17e+01
  bond pdb=" N   LEU A  79 "
       pdb=" CA  LEU A  79 "
    ideal  model  delta    sigma   weight residual
    1.456  1.498 -0.041 1.31e-02 5.83e+03 9.86e+00
  bond pdb=" N   HIS A 401 "
       pdb=" CA  HIS A 401 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.30e-02 5.92e+03 7.66e+00
  bond pdb=" N   SER B 494 "
       pdb=" CA  SER B 494 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.23e-02 6.61e+03 6.31e+00
  ... (remaining 6739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 8782
        1.27 -     2.55: 292
        2.55 -     3.82: 70
        3.82 -     5.09: 20
        5.09 -     6.36: 6
  Bond angle restraints: 9170
  Sorted by residual:
  angle pdb=" N   GLU A 227 "
        pdb=" CA  GLU A 227 "
        pdb=" CB  GLU A 227 "
      ideal   model   delta    sigma   weight residual
     110.12  115.10   -4.98 1.47e+00 4.63e-01 1.15e+01
  angle pdb=" N   LYS A 419 "
        pdb=" CA  LYS A 419 "
        pdb=" C   LYS A 419 "
      ideal   model   delta    sigma   weight residual
     111.36  107.81    3.55 1.09e+00 8.42e-01 1.06e+01
  angle pdb=" C   ASN B 487 "
        pdb=" CA  ASN B 487 "
        pdb=" CB  ASN B 487 "
      ideal   model   delta    sigma   weight residual
     110.42  116.78   -6.36 1.99e+00 2.53e-01 1.02e+01
  angle pdb=" C   GLN A  24 "
        pdb=" N   ALA A  25 "
        pdb=" CA  ALA A  25 "
      ideal   model   delta    sigma   weight residual
     120.29  124.78   -4.49 1.42e+00 4.96e-01 1.00e+01
  angle pdb=" N   ASN B 487 "
        pdb=" CA  ASN B 487 "
        pdb=" C   ASN B 487 "
      ideal   model   delta    sigma   weight residual
     110.80  104.71    6.09 2.13e+00 2.20e-01 8.18e+00
  ... (remaining 9165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 3709
       17.33 -    34.66: 307
       34.66 -    51.99: 68
       51.99 -    69.32: 15
       69.32 -    86.65: 7
  Dihedral angle restraints: 4106
    sinusoidal: 1780
      harmonic: 2326
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.93   55.07     1      1.00e+01 1.00e-02 4.10e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.81  -48.81     1      1.00e+01 1.00e-02 3.28e+01
  dihedral pdb=" CA  CYS A 141 "
           pdb=" C   CYS A 141 "
           pdb=" N   LEU A 142 "
           pdb=" CA  LEU A 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.05  -21.95     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 4103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 709
       0.043 -    0.087: 206
       0.087 -    0.130: 64
       0.130 -    0.173: 6
       0.173 -    0.216: 2
  Chirality restraints: 987
  Sorted by residual:
  chirality pdb=" C1  NAG A 902 "
            pdb=" ND2 ASN A  90 "
            pdb=" C2  NAG A 902 "
            pdb=" O5  NAG A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  ILE B 410 "
            pdb=" CA  ILE B 410 "
            pdb=" CG1 ILE B 410 "
            pdb=" CG2 ILE B 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.97e-01
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 984 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 486 "   -0.015 2.00e-02 2.50e+03   2.94e-02 8.66e+00
        pdb=" C   VAL B 486 "    0.051 2.00e-02 2.50e+03
        pdb=" O   VAL B 486 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN B 487 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 302 "   -0.017 2.00e-02 2.50e+03   1.69e-02 7.18e+00
        pdb=" CG  TRP A 302 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 302 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 302 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 302 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 302 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 302 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 302 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 302 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 302 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 400 "    0.013 2.00e-02 2.50e+03   2.45e-02 6.01e+00
        pdb=" C   PHE A 400 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   PHE A 400 "    0.015 2.00e-02 2.50e+03
        pdb=" N   HIS A 401 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 38
        2.58 -     3.16: 5188
        3.16 -     3.74: 9740
        3.74 -     4.32: 13628
        4.32 -     4.90: 22976
  Nonbonded interactions: 51570
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 905 "
     model   vdw
     2.004 2.230
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" NZ  LYS A 288 "
            pdb=" OD2 ASP A 431 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ILE A 151 "
            pdb=" OG  SER A 155 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OD1 ASN A  90 "
            pdb=" N2  NAG A 902 "
     model   vdw
     2.318 3.120
  ... (remaining 51565 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     24.050
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:13.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.210   6763  Z= 0.223
  Angle     :  0.607   8.126   9214  Z= 0.316
  Chirality :  0.044   0.216    987
  Planarity :  0.004   0.055   1176
  Dihedral  : 13.558  86.655   2593
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.43 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.07 (0.30), residues: 788
  helix:  1.02 (0.27), residues: 356
  sheet:  1.71 (0.75), residues: 50
  loop : -1.15 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 302 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 308 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.002   0.000   ARG A 559 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00556 (    7)
  link_NAG-ASN         : angle       2.72611 (   21)
  link_BETA1-4         : bond        0.00382 (    2)
  link_BETA1-4         : angle       0.86038 (    6)
  hydrogen bonds       : bond        0.16795 (  290)
  hydrogen bonds       : angle       5.98054 (  821)
  link_BETA1-6         : bond        0.00400 (    1)
  link_BETA1-6         : angle       1.32768 (    3)
  metal coordination   : bond        0.20377 (    2)
  SS BOND              : bond        0.00299 (    7)
  SS BOND              : angle       0.79712 (   14)
  covalent geometry    : bond        0.00358 ( 6744)
  covalent geometry    : angle       0.59220 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 179
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: A  483 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6992 (tm-30)
REVERT: A  549 GLU cc_start: 0.7445 (mp0) cc_final: 0.7150 (mp0)
REVERT: B  438 SER cc_start: 0.8205 (t) cc_final: 0.7900 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 180
  average time/residue: 1.0636
  time to fit residues: 202.2002
Evaluate side-chains
  156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  417 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0070
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
A 175 GLN
A 210 ASN
A 374 HIS
A 394 ASN
A 401 HIS
A 580 ASN
B 417 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113601 restraints weight = 16197.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.94
r_work: 0.3354 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3360
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3360 r_free = 0.3360    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.778   6763  Z= 0.345
  Angle     :  0.589   9.821   9214  Z= 0.295
  Chirality :  0.043   0.199    987
  Planarity :  0.004   0.037   1176
  Dihedral  :  6.031  53.935   1070
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.67 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.18 (0.30), residues: 788
  helix:  1.21 (0.28), residues: 367
  sheet:  0.95 (0.73), residues: 48
  loop : -1.13 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 302 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.017   0.001   PHE B 400 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.004   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00669 (    7)
  link_NAG-ASN         : angle       2.97623 (   21)
  link_BETA1-4         : bond        0.00565 (    2)
  link_BETA1-4         : angle       1.15485 (    6)
  hydrogen bonds       : bond        0.05274 (  290)
  hydrogen bonds       : angle       4.68378 (  821)
  link_BETA1-6         : bond        0.00417 (    1)
  link_BETA1-6         : angle       1.21814 (    3)
  metal coordination   : bond        0.55039 (    2)
  SS BOND              : bond        0.00422 (    7)
  SS BOND              : angle       0.69082 (   14)
  covalent geometry    : bond        0.00309 ( 6744)
  covalent geometry    : angle       0.57120 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 164
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7174 (tm-30)
REVERT: A  549 GLU cc_start: 0.7686 (mp0) cc_final: 0.7466 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 167
  average time/residue: 1.1083
  time to fit residues: 195.0489
Evaluate side-chains
  163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 160
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  402 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0000
   chunk 70 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.5382

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 188 ASN
A 374 HIS
A 580 ASN
B 417 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.118986 restraints weight = 8896.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.08
r_work: 0.3423 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.792   6763  Z= 0.345
  Angle     :  0.552   8.098   9214  Z= 0.275
  Chirality :  0.042   0.199    987
  Planarity :  0.004   0.034   1176
  Dihedral  :  5.753  54.699   1068
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.12 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.16 (0.30), residues: 788
  helix:  1.27 (0.28), residues: 373
  sheet:  0.62 (0.80), residues: 38
  loop : -1.17 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 478 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.015   0.001   PHE B 400 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.003   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00579 (    7)
  link_NAG-ASN         : angle       2.84998 (   21)
  link_BETA1-4         : bond        0.00477 (    2)
  link_BETA1-4         : angle       1.02901 (    6)
  hydrogen bonds       : bond        0.04822 (  290)
  hydrogen bonds       : angle       4.42816 (  821)
  link_BETA1-6         : bond        0.00438 (    1)
  link_BETA1-6         : angle       1.14029 (    3)
  metal coordination   : bond        0.55979 (    2)
  SS BOND              : bond        0.00374 (    7)
  SS BOND              : angle       0.66128 (   14)
  covalent geometry    : bond        0.00280 ( 6744)
  covalent geometry    : angle       0.53490 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: A  171 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7502 (mt-10)
REVERT: A  549 GLU cc_start: 0.7817 (mp0) cc_final: 0.7598 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 165
  average time/residue: 1.1164
  time to fit residues: 194.0058
Evaluate side-chains
  167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 159
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0980
   chunk 68 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 210 ASN
A 580 ASN
B 417 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.142024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119038 restraints weight = 11080.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.37
r_work: 0.3390 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6763  Z= 0.132
  Angle     :  0.543   7.895   9214  Z= 0.271
  Chirality :  0.043   0.206    987
  Planarity :  0.004   0.031   1176
  Dihedral  :  5.540  53.849   1068
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.05 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.85 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.22 (0.30), residues: 788
  helix:  1.33 (0.28), residues: 371
  sheet:  0.47 (0.80), residues: 38
  loop : -1.12 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 478 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.012   0.001   PHE A 327 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.003   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00577 (    7)
  link_NAG-ASN         : angle       2.79147 (   21)
  link_BETA1-4         : bond        0.00504 (    2)
  link_BETA1-4         : angle       1.05455 (    6)
  hydrogen bonds       : bond        0.04801 (  290)
  hydrogen bonds       : angle       4.29301 (  821)
  link_BETA1-6         : bond        0.00412 (    1)
  link_BETA1-6         : angle       1.14144 (    3)
  metal coordination   : bond        0.01267 (    2)
  SS BOND              : bond        0.00401 (    7)
  SS BOND              : angle       0.72144 (   14)
  covalent geometry    : bond        0.00300 ( 6744)
  covalent geometry    : angle       0.52586 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7447 (tm-30)
REVERT: A  549 GLU cc_start: 0.7837 (mp0) cc_final: 0.7617 (mp0)
REVERT: B  355 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7324 (ttt-90)
  outliers start: 11
  outliers final: 6
  residues processed: 159
  average time/residue: 1.1275
  time to fit residues: 188.8408
Evaluate side-chains
  166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0770
   chunk 5 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0980
   chunk 77 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 580 ASN
B 417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.142664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.119124 restraints weight = 13241.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 2.59
r_work: 0.3381 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6763  Z= 0.112
  Angle     :  0.530   7.884   9214  Z= 0.263
  Chirality :  0.042   0.209    987
  Planarity :  0.003   0.031   1176
  Dihedral  :  5.248  53.446   1068
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.42 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.23 (0.30), residues: 788
  helix:  1.37 (0.28), residues: 373
  sheet:  0.35 (0.81), residues: 38
  loop : -1.14 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 478 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.012   0.001   PHE B 400 
 TYR   0.010   0.001   TYR A 183 
 ARG   0.006   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00606 (    7)
  link_NAG-ASN         : angle       2.75467 (   21)
  link_BETA1-4         : bond        0.00458 (    2)
  link_BETA1-4         : angle       1.07107 (    6)
  hydrogen bonds       : bond        0.04448 (  290)
  hydrogen bonds       : angle       4.22002 (  821)
  link_BETA1-6         : bond        0.00413 (    1)
  link_BETA1-6         : angle       1.14721 (    3)
  metal coordination   : bond        0.00285 (    2)
  SS BOND              : bond        0.00368 (    7)
  SS BOND              : angle       0.69138 (   14)
  covalent geometry    : bond        0.00246 ( 6744)
  covalent geometry    : angle       0.51230 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7513 (tm-30)
REVERT: A  167 SER cc_start: 0.8763 (m) cc_final: 0.8019 (m)
REVERT: A  171 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7521 (mp0)
REVERT: A  549 GLU cc_start: 0.7845 (mp0) cc_final: 0.7627 (mp0)
REVERT: B  355 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7358 (ttt-90)
  outliers start: 16
  outliers final: 8
  residues processed: 162
  average time/residue: 1.0656
  time to fit residues: 182.1506
Evaluate side-chains
  168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   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 175 GLN
A 188 ASN
A 210 ASN
A 580 ASN
B 417 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.140518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.116693 restraints weight = 16273.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.80
r_work: 0.3339 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6763  Z= 0.155
  Angle     :  0.557   8.243   9214  Z= 0.277
  Chirality :  0.044   0.225    987
  Planarity :  0.004   0.037   1176
  Dihedral  :  5.104  53.699   1068
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.99 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.15 (0.30), residues: 788
  helix:  1.26 (0.27), residues: 373
  sheet:  0.26 (0.80), residues: 38
  loop : -1.14 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 478 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.014   0.001   PHE A 327 
 TYR   0.019   0.002   TYR A 454 
 ARG   0.009   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00575 (    7)
  link_NAG-ASN         : angle       2.76628 (   21)
  link_BETA1-4         : bond        0.00508 (    2)
  link_BETA1-4         : angle       1.12009 (    6)
  hydrogen bonds       : bond        0.05004 (  290)
  hydrogen bonds       : angle       4.24533 (  821)
  link_BETA1-6         : bond        0.00461 (    1)
  link_BETA1-6         : angle       1.15762 (    3)
  metal coordination   : bond        0.00439 (    2)
  SS BOND              : bond        0.00408 (    7)
  SS BOND              : angle       0.77282 (   14)
  covalent geometry    : bond        0.00359 ( 6744)
  covalent geometry    : angle       0.54084 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 153
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7206 (tm-30)
REVERT: A  167 SER cc_start: 0.8684 (m) cc_final: 0.8429 (m)
REVERT: A  549 GLU cc_start: 0.7644 (mp0) cc_final: 0.7410 (mp0)
REVERT: B  355 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7268 (mtt-85)
REVERT: B  503 VAL cc_start: 0.8541 (p) cc_final: 0.8289 (t)
  outliers start: 15
  outliers final: 9
  residues processed: 156
  average time/residue: 1.1120
  time to fit residues: 182.9641
Evaluate side-chains
  166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 580 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.117631 restraints weight = 11056.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 2.28
r_work: 0.3376 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6763  Z= 0.158
  Angle     :  0.568   8.131   9214  Z= 0.281
  Chirality :  0.044   0.223    987
  Planarity :  0.004   0.034   1176
  Dihedral  :  5.044  53.552   1068
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.54 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.57 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.12 (0.30), residues: 788
  helix:  1.24 (0.27), residues: 373
  sheet:  0.16 (0.80), residues: 38
  loop : -1.13 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 436 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.014   0.001   PHE A 327 
 TYR   0.012   0.002   TYR A 385 
 ARG   0.008   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00525 (    7)
  link_NAG-ASN         : angle       2.78717 (   21)
  link_BETA1-4         : bond        0.00372 (    2)
  link_BETA1-4         : angle       1.09792 (    6)
  hydrogen bonds       : bond        0.05071 (  290)
  hydrogen bonds       : angle       4.26638 (  821)
  link_BETA1-6         : bond        0.00412 (    1)
  link_BETA1-6         : angle       1.15695 (    3)
  metal coordination   : bond        0.00418 (    2)
  SS BOND              : bond        0.00418 (    7)
  SS BOND              : angle       0.79524 (   14)
  covalent geometry    : bond        0.00369 ( 6744)
  covalent geometry    : angle       0.55140 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7431 (tm-30)
REVERT: A  167 SER cc_start: 0.8745 (m) cc_final: 0.8497 (m)
REVERT: A  549 GLU cc_start: 0.7828 (mp0) cc_final: 0.7600 (mp0)
REVERT: B  355 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7365 (mtt-85)
REVERT: B  503 VAL cc_start: 0.8602 (p) cc_final: 0.8332 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 163
  average time/residue: 1.0354
  time to fit residues: 178.0542
Evaluate side-chains
  170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0570
   chunk 37 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0070
   chunk 53 optimal weight:    0.7980
   chunk 74 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0030
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.1726

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 580 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 = 0.3868 r_free = 0.3868 target = 0.143468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.119268 restraints weight = 16359.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.88
r_work: 0.3369 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6763  Z= 0.102
  Angle     :  0.534   7.708   9214  Z= 0.261
  Chirality :  0.041   0.196    987
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.841  53.164   1068
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.67 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 17.72 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.29 (0.30), residues: 788
  helix:  1.40 (0.27), residues: 375
  sheet:  0.11 (0.80), residues: 38
  loop : -1.07 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 436 
 HIS   0.005   0.001   HIS A 241 
 PHE   0.011   0.001   PHE A 327 
 TYR   0.011   0.001   TYR A 510 
 ARG   0.008   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00582 (    7)
  link_NAG-ASN         : angle       2.66878 (   21)
  link_BETA1-4         : bond        0.00476 (    2)
  link_BETA1-4         : angle       1.09395 (    6)
  hydrogen bonds       : bond        0.04068 (  290)
  hydrogen bonds       : angle       4.15548 (  821)
  link_BETA1-6         : bond        0.00317 (    1)
  link_BETA1-6         : angle       1.15849 (    3)
  metal coordination   : bond        0.00062 (    2)
  SS BOND              : bond        0.00343 (    7)
  SS BOND              : angle       0.69328 (   14)
  covalent geometry    : bond        0.00211 ( 6744)
  covalent geometry    : angle       0.51767 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: A  167 SER cc_start: 0.8666 (m) cc_final: 0.8408 (m)
REVERT: A  227 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7600 (mm-30)
REVERT: B  355 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7233 (mtt-85)
REVERT: B  503 VAL cc_start: 0.8549 (p) cc_final: 0.8301 (t)
  outliers start: 10
  outliers final: 6
  residues processed: 163
  average time/residue: 1.0585
  time to fit residues: 182.3878
Evaluate side-chains
  164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 157
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 ASN
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0050
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 580 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 = 0.3842 r_free = 0.3842 target = 0.140514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.115992 restraints weight = 17607.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.96
r_work: 0.3338 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6763  Z= 0.133
  Angle     :  0.559   7.458   9214  Z= 0.274
  Chirality :  0.043   0.202    987
  Planarity :  0.004   0.032   1176
  Dihedral  :  4.865  53.303   1068
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 18.88 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.32 (0.30), residues: 788
  helix:  1.36 (0.27), residues: 381
  sheet:  0.24 (0.81), residues: 38
  loop : -1.03 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.014   0.001   PHE A 327 
 TYR   0.024   0.001   TYR A 183 
 ARG   0.007   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00482 (    7)
  link_NAG-ASN         : angle       2.58748 (   21)
  link_BETA1-4         : bond        0.00391 (    2)
  link_BETA1-4         : angle       1.09932 (    6)
  hydrogen bonds       : bond        0.04632 (  290)
  hydrogen bonds       : angle       4.17453 (  821)
  link_BETA1-6         : bond        0.00394 (    1)
  link_BETA1-6         : angle       1.16973 (    3)
  metal coordination   : bond        0.00342 (    2)
  SS BOND              : bond        0.00383 (    7)
  SS BOND              : angle       0.74855 (   14)
  covalent geometry    : bond        0.00306 ( 6744)
  covalent geometry    : angle       0.54409 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7190 (tm-30)
REVERT: A  167 SER cc_start: 0.8667 (m) cc_final: 0.8395 (m)
REVERT: B  355 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7263 (mtt-85)
REVERT: B  503 VAL cc_start: 0.8540 (p) cc_final: 0.8286 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 163
  average time/residue: 1.0768
  time to fit residues: 185.6807
Evaluate side-chains
  166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 56 optimal weight:    0.3980
   chunk 61 optimal weight:    0.0870
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A 580 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 = 0.3858 r_free = 0.3858 target = 0.141722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.117730 restraints weight = 17643.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.93
r_work: 0.3350 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6763  Z= 0.118
  Angle     :  0.553   7.613   9214  Z= 0.271
  Chirality :  0.042   0.201    987
  Planarity :  0.004   0.032   1176
  Dihedral  :  4.817  53.252   1068
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 19.31 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.33 (0.30), residues: 788
  helix:  1.38 (0.27), residues: 380
  sheet:  0.16 (0.81), residues: 38
  loop : -1.02 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 436 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.014   0.001   PHE B 400 
 TYR   0.021   0.001   TYR A 183 
 ARG   0.007   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00552 (    7)
  link_NAG-ASN         : angle       2.54990 (   21)
  link_BETA1-4         : bond        0.00397 (    2)
  link_BETA1-4         : angle       1.08602 (    6)
  hydrogen bonds       : bond        0.04364 (  290)
  hydrogen bonds       : angle       4.17653 (  821)
  link_BETA1-6         : bond        0.00351 (    1)
  link_BETA1-6         : angle       1.15935 (    3)
  metal coordination   : bond        0.00158 (    2)
  SS BOND              : bond        0.00362 (    7)
  SS BOND              : angle       0.72209 (   14)
  covalent geometry    : bond        0.00263 ( 6744)
  covalent geometry    : angle       0.53913 ( 9170)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 157
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7210 (tm-30)
REVERT: A  167 SER cc_start: 0.8661 (m) cc_final: 0.8408 (m)
REVERT: B  355 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7244 (mtt-85)
REVERT: B  489 TYR cc_start: 0.7389 (m-80) cc_final: 0.7066 (m-80)
REVERT: B  503 VAL cc_start: 0.8549 (p) cc_final: 0.8298 (t)
  outliers start: 8
  outliers final: 7
  residues processed: 160
  average time/residue: 1.0294
  time to fit residues: 174.0792
Evaluate side-chains
  165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 158
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  292 ASP
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  347 PHE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0370
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A 580 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 = 0.3865 r_free = 0.3865 target = 0.142302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.119499 restraints weight = 12945.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.48
r_work: 0.3397 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6763  Z= 0.110
  Angle     :  0.546   7.919   9214  Z= 0.266
  Chirality :  0.042   0.199    987
  Planarity :  0.003   0.032   1176
  Dihedral  :  4.771  53.279   1068
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.41 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 18.73 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.44 (0.30), residues: 788
  helix:  1.48 (0.27), residues: 375
  sheet:  0.20 (0.81), residues: 38
  loop : -0.95 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 436 
 HIS   0.006   0.001   HIS A 241 
 PHE   0.012   0.001   PHE A 327 
 TYR   0.014   0.001   TYR A 183 
 ARG   0.007   0.000   ARG A 192 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00473 (    7)
  link_NAG-ASN         : angle       2.53745 (   21)
  link_BETA1-4         : bond        0.00369 (    2)
  link_BETA1-4         : angle       1.07501 (    6)
  hydrogen bonds       : bond        0.04172 (  290)
  hydrogen bonds       : angle       4.11164 (  821)
  link_BETA1-6         : bond        0.00366 (    1)
  link_BETA1-6         : angle       1.17019 (    3)
  metal coordination   : bond        0.00196 (    2)
  SS BOND              : bond        0.00353 (    7)
  SS BOND              : angle       0.70935 (   14)
  covalent geometry    : bond        0.00244 ( 6744)
  covalent geometry    : angle       0.53139 ( 9170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6302.87 seconds
wall clock time: 107 minutes 34.86 seconds (6454.86 seconds total)