Starting phenix.real_space_refine
on Thu May 15 13:38:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uw8_42639/05_2025/8uw8_42639_trim.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      46      5.16       5
     C    4177      2.51       5
     N    1125      2.21       5
     O    1317      1.98       5
     H    6464      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13130
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 11397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 738, 11397
          Classifications: {'peptide': 738}
          Link IDs: {'PCIS': 9, 'PTRANS': 38, 'TRANS': 690}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 1454
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 231
          Unusual residues: {' CA': 1, 'NAG': 1}
          Classifications: {'undetermined': 2, 'water': 72}
          Link IDs: {None: 73}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 9
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 11.03, per 1000 atoms: 0.84
  Number of scatterers: 13130
  At special positions: 0
  Unit cell: (80.25, 91.485, 94.695, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      46     16.00
     O    1317      8.00
     N    1125      7.00
     C    4177      6.00
     H    6464      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 263 " - pdb=" SG  CYS A 407 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 501 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 684 " - pdb=" SG  CYS A 927 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 849 " - pdb=" SG  CYS A 859 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  75 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 116 " - pdb=" SG  CYS B 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 119 " - pdb=" SG  CYS B 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 124 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 169 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG C   1 " - " ASN A 515 "
  Time building additional restraints: 3.65
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1526

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      28.3% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 192 through 197
    Processing helix  chain 'A' and resid 198 through 204
      removed outlier: 3.784A  pdb=" N   LEU A 202 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 259
    Processing helix  chain 'A' and resid 285 through 300
    Processing helix  chain 'A' and resid 315 through 328
    Processing helix  chain 'A' and resid 412 through 431
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'A' and resid 438 through 450
    Processing helix  chain 'A' and resid 457 through 462
    Processing helix  chain 'A' and resid 467 through 478
    Processing helix  chain 'A' and resid 541 through 543
      No H-bonds generated for 'chain 'A' and resid 541 through 543'
    Processing helix  chain 'A' and resid 570 through 575
      removed outlier: 3.925A  pdb=" N   SER A 574 " --> pdb=" O   LYS A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 671
    Processing helix  chain 'A' and resid 681 through 685
      removed outlier: 3.766A  pdb=" N   PHE A 685 " --> pdb=" O   PHE A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 728 through 735
    Processing helix  chain 'A' and resid 754 through 763
    Processing helix  chain 'A' and resid 764 through 766
      No H-bonds generated for 'chain 'A' and resid 764 through 766'
    Processing helix  chain 'A' and resid 810 through 817
    Processing helix  chain 'A' and resid 859 through 873
    Processing helix  chain 'A' and resid 876 through 881
    Processing helix  chain 'A' and resid 904 through 909
      removed outlier: 3.701A  pdb=" N   SER A 909 " --> pdb=" O   HIS A 906 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 98
      No H-bonds generated for 'chain 'B' and resid 96 through 98'
    Processing helix  chain 'B' and resid 127 through 136
    Processing helix  chain 'B' and resid 166 through 173
    Processing helix  chain 'B' and resid 176 through 178
      No H-bonds generated for 'chain 'B' and resid 176 through 178'
    Processing helix  chain 'B' and resid 188 through 192
      removed outlier: 3.560A  pdb=" N   LYS B 192 " --> pdb=" O   PRO B 189 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 236
      removed outlier: 4.689A  pdb=" N   VAL A 231 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   ILE A 274 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   GLU A 233 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   ARG A 276 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   THR A 235 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ARG A 213 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   ASN A 305 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ALA A 215 " --> pdb=" O   ASN A 305 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   LEU A 304 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   ALA A 335 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   LEU A 306 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   MET A 332 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
      removed outlier: 7.369A  pdb=" N   VAL A 358 " --> pdb=" O   MET A 332 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   SER A 334 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 8.493A  pdb=" N   GLY A 360 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ILE A 391 " --> pdb=" O   VAL A 355 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   GLY A 357 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   THR A 393 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 6.077A  pdb=" N   GLY A 359 " --> pdb=" O   THR A 393 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   GLY A 395 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   GLY A 397 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 482 through 485
    Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490
    Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 506
    Processing sheet with id=AA5, first strand: chain 'A' and resid 674 through 678
      removed outlier: 4.249A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 622 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   VAL A 696 " --> pdb=" O   ASP A 626 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU A 693 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   PHE A 723 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   MET A 695 " --> pdb=" O   PHE A 723 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   VAL A 821 " --> pdb=" O   ASP A 809 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ASP A 809 " --> pdb=" O   VAL A 821 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   GLU A 823 " --> pdb=" O   PHE A 807 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   PHE A 807 " --> pdb=" O   GLU A 823 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN A 805 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE A 827 " --> pdb=" O   ILE A 803 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   ILE A 803 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 8.420A  pdb=" N   THR A 804 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 8.853A  pdb=" N   THR A 779 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   THR A 806 " --> pdb=" O   GLU A 777 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLU A 777 " --> pdb=" O   THR A 806 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   TYR A 774 " --> pdb=" O   SER A 789 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   SER A 789 " --> pdb=" O   TYR A 774 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   PHE A 778 " --> pdb=" O   MET A 785 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 739
    Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 86
      removed outlier: 3.771A  pdb=" N   LYS B 112 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125
    Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 181

    226 hydrogen bonds defined for protein.
    612 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: 5.43

  Time building geometry restraints manager: 4.37 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6462
        1.03 -     1.23: 31
        1.23 -     1.42: 2874
        1.42 -     1.62: 3793
        1.62 -     1.81: 68
  Bond restraints: 13228
  Sorted by residual:
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.567 -0.048 2.00e-02 2.50e+03 5.69e+00
  bond pdb=" C5  NAG A1101 "
       pdb=" O5  NAG A1101 "
    ideal  model  delta    sigma   weight residual
    1.413  1.437 -0.024 2.00e-02 2.50e+03 1.41e+00
  bond pdb=" CB  CYS A 494 "
       pdb=" SG  CYS A 494 "
    ideal  model  delta    sigma   weight residual
    1.808  1.771  0.037 3.30e-02 9.18e+02 1.28e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.27e+00
  bond pdb=" CG  PRO A 634 "
       pdb=" CD  PRO A 634 "
    ideal  model  delta    sigma   weight residual
    1.512  1.482  0.030 2.70e-02 1.37e+03 1.22e+00
  ... (remaining 13223 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 23337
        1.86 -     3.71: 271
        3.71 -     5.57: 26
        5.57 -     7.42: 3
        7.42 -     9.28: 1
  Bond angle restraints: 23638
  Sorted by residual:
  angle pdb=" N   ILE A 827 "
        pdb=" CA  ILE A 827 "
        pdb=" C   ILE A 827 "
      ideal   model   delta    sigma   weight residual
     113.53  109.52    4.01 9.80e-01 1.04e+00 1.67e+01
  angle pdb=" N   PRO A 634 "
        pdb=" CA  PRO A 634 "
        pdb=" C   PRO A 634 "
      ideal   model   delta    sigma   weight residual
     112.10  121.38   -9.28 2.60e+00 1.48e-01 1.27e+01
  angle pdb=" C   THR A 659 "
        pdb=" N   ASN A 660 "
        pdb=" CA  ASN A 660 "
      ideal   model   delta    sigma   weight residual
     121.54  127.24   -5.70 1.91e+00 2.74e-01 8.92e+00
  angle pdb=" CA  ILE A 827 "
        pdb=" C   ILE A 827 "
        pdb=" N   LEU A 828 "
      ideal   model   delta    sigma   weight residual
     119.31  116.31    3.00 1.15e+00 7.56e-01 6.80e+00
  angle pdb=" C   TYR A 633 "
        pdb=" N   PRO A 634 "
        pdb=" CA  PRO A 634 "
      ideal   model   delta    sigma   weight residual
     127.00  132.53   -5.53 2.40e+00 1.74e-01 5.30e+00
  ... (remaining 23633 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.96: 5843
       21.96 -    43.93: 370
       43.93 -    65.89: 84
       65.89 -    87.86: 12
       87.86 -   109.82: 5
  Dihedral angle restraints: 6314
    sinusoidal: 3441
      harmonic: 2873
  Sorted by residual:
  dihedral pdb=" CA  ARG A 632 "
           pdb=" C   ARG A 632 "
           pdb=" N   TYR A 633 "
           pdb=" CA  TYR A 633 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.31   20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CB  CYS A 849 "
           pdb=" SG  CYS A 849 "
           pdb=" SG  CYS A 859 "
           pdb=" CB  CYS A 859 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   58.87   34.13     1      1.00e+01 1.00e-02 1.65e+01
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     288.71  178.89  109.82     1      3.00e+01 1.11e-03 1.43e+01
  ... (remaining 6311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 861
       0.064 -    0.128: 129
       0.128 -    0.193: 4
       0.193 -    0.257: 1
       0.257 -    0.321: 2
  Chirality restraints: 997
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 515 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.08   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  PRO A 634 "
            pdb=" N   PRO A 634 "
            pdb=" C   PRO A 634 "
            pdb=" CB  PRO A 634 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.91e-01
  ... (remaining 994 not shown)

  Planarity restraints: 1974
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 614 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 615 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 615 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 615 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 637 "   -0.008 2.00e-02 2.50e+03   7.39e-03 1.64e+00
        pdb=" CG  TYR A 637 "    0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 637 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 637 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 637 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 637 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 637 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 637 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 637 "    0.000 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 637 "    0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 637 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 637 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 515 "   -0.013 2.00e-02 2.50e+03   1.01e-02 1.54e+00
        pdb=" CG  ASN A 515 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 515 "   -0.002 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 515 "    0.009 2.00e-02 2.50e+03
        pdb="HD21 ASN A 515 "    0.003 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1971 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 486
        2.12 -     2.74: 24273
        2.74 -     3.36: 40663
        3.36 -     3.98: 55220
        3.98 -     4.60: 84470
  Nonbonded interactions: 205112
  Sorted by model distance:
  nonbonded pdb=" H   SER A 724 "
            pdb=" O   TYR A 844 "
     model   vdw
     1.501 2.450
  nonbonded pdb=" HE1 TRP A 556 "
            pdb=" O   GLN B  80 "
     model   vdw
     1.522 2.450
  nonbonded pdb="HD21 ASN A 728 "
            pdb=" O   ASP A 771 "
     model   vdw
     1.522 2.450
  nonbonded pdb=" O   GLU A 324 "
            pdb="HD21 ASN A 328 "
     model   vdw
     1.526 2.450
  nonbonded pdb=" OD1 ASN A 305 "
            pdb=" HG  SER A 417 "
     model   vdw
     1.546 2.450
  ... (remaining 205107 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             24.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.250
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     36.990
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   74.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
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      :  0.004   0.048   6778  Z= 0.187
  Angle     :  0.655  10.056   9234  Z= 0.332
  Chirality :  0.046   0.321    997
  Planarity :  0.004   0.043   1193
  Dihedral  : 14.409 109.823   2518
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.89 (0.28), residues: 827
  helix:  0.60 (0.37), residues: 187
  sheet: -1.56 (0.40), residues: 131
  loop : -0.74 (0.28), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 378 
 HIS   0.003   0.001   HIS B  83 
 PHE   0.018   0.002   PHE A 638 
 TYR   0.021   0.002   TYR A 637 
 ARG   0.005   0.000   ARG A 527 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01152 (    1)
  link_NAG-ASN         : angle       8.59897 (    3)
  link_BETA1-4         : bond        0.01883 (    2)
  link_BETA1-4         : angle       4.85492 (    6)
  hydrogen bonds       : bond        0.13485 (  214)
  hydrogen bonds       : angle       8.28394 (  612)
  SS BOND              : bond        0.00320 (   11)
  SS BOND              : angle       1.38420 (   22)
  covalent geometry    : bond        0.00399 ( 6764)
  covalent geometry    : angle       0.62156 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 148
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 148
  average time/residue: 2.1019
  time to fit residues: 331.6304
Evaluate side-chains
  103 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  515 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.0000
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4542

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
A 766 ASN
A 783 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.122361 restraints weight = 27583.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 2.39
r_work: 0.3573 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6778  Z= 0.155
  Angle     :  0.637   8.770   9234  Z= 0.321
  Chirality :  0.045   0.177    997
  Planarity :  0.005   0.044   1193
  Dihedral  :  8.297  65.159    994
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.69 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.88 (0.29), residues: 827
  helix:  0.61 (0.36), residues: 192
  sheet: -1.57 (0.42), residues: 129
  loop : -0.75 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 861 
 HIS   0.004   0.001   HIS A 225 
 PHE   0.016   0.002   PHE A 737 
 TYR   0.011   0.001   TYR A 869 
 ARG   0.008   0.001   ARG A 840 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01059 (    1)
  link_NAG-ASN         : angle       7.27056 (    3)
  link_BETA1-4         : bond        0.00924 (    2)
  link_BETA1-4         : angle       3.21289 (    6)
  hydrogen bonds       : bond        0.04639 (  214)
  hydrogen bonds       : angle       6.91459 (  612)
  SS BOND              : bond        0.00500 (   11)
  SS BOND              : angle       1.09831 (   22)
  covalent geometry    : bond        0.00336 ( 6764)
  covalent geometry    : angle       0.61630 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 3
  residues processed: 112
  average time/residue: 1.8257
  time to fit residues: 220.4728
Evaluate side-chains
  101 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  281 ASN
Chi-restraints excluded: chain A residue  515 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.138430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.120472 restraints weight = 27897.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.39
r_work: 0.3555 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6778  Z= 0.196
  Angle     :  0.647   9.092   9234  Z= 0.326
  Chirality :  0.045   0.189    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  6.621  55.627    994
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.39 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.99 (0.28), residues: 827
  helix:  0.52 (0.36), residues: 191
  sheet: -1.56 (0.41), residues: 131
  loop : -0.85 (0.28), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 861 
 HIS   0.005   0.001   HIS A 225 
 PHE   0.015   0.002   PHE A 638 
 TYR   0.013   0.001   TYR A 774 
 ARG   0.004   0.001   ARG A 840 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00917 (    1)
  link_NAG-ASN         : angle       7.78532 (    3)
  link_BETA1-4         : bond        0.01102 (    2)
  link_BETA1-4         : angle       3.08136 (    6)
  hydrogen bonds       : bond        0.04277 (  214)
  hydrogen bonds       : angle       6.57678 (  612)
  SS BOND              : bond        0.00303 (   11)
  SS BOND              : angle       1.15354 (   22)
  covalent geometry    : bond        0.00431 ( 6764)
  covalent geometry    : angle       0.62491 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  900 MET cc_start: 0.8397 (ttp) cc_final: 0.8046 (mtp)
  outliers start: 6
  outliers final: 5
  residues processed: 106
  average time/residue: 1.7935
  time to fit residues: 204.9496
Evaluate side-chains
  101 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  281 ASN
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  660 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 34 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 8 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 236 ASN
A 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.139001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.121114 restraints weight = 27649.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.39
r_work: 0.3567 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6778  Z= 0.163
  Angle     :  0.633   8.875   9234  Z= 0.318
  Chirality :  0.045   0.178    997
  Planarity :  0.005   0.044   1193
  Dihedral  :  6.088  57.540    994
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.52 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.92 (0.29), residues: 827
  helix:  0.63 (0.37), residues: 192
  sheet: -1.58 (0.42), residues: 129
  loop : -0.82 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 861 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.022   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01207 (    1)
  link_NAG-ASN         : angle       7.44262 (    3)
  link_BETA1-4         : bond        0.00782 (    2)
  link_BETA1-4         : angle       2.59141 (    6)
  hydrogen bonds       : bond        0.03904 (  214)
  hydrogen bonds       : angle       6.39705 (  612)
  SS BOND              : bond        0.00246 (   11)
  SS BOND              : angle       1.80179 (   22)
  covalent geometry    : bond        0.00360 ( 6764)
  covalent geometry    : angle       0.60983 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  900 MET cc_start: 0.8388 (ttp) cc_final: 0.8044 (mtp)
  outliers start: 7
  outliers final: 5
  residues processed: 104
  average time/residue: 2.0525
  time to fit residues: 228.0679
Evaluate side-chains
  99 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  660 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 77 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   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 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.137833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.120128 restraints weight = 28198.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.38
r_work: 0.3556 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6778  Z= 0.195
  Angle     :  0.646   9.045   9234  Z= 0.324
  Chirality :  0.045   0.188    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  6.080  57.572    994
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.94 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.29), residues: 827
  helix:  0.56 (0.37), residues: 192
  sheet: -1.63 (0.42), residues: 129
  loop : -0.86 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 932 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.015   0.002   PHE A 638 
 TYR   0.011   0.001   TYR A 774 
 ARG   0.005   0.001   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00921 (    1)
  link_NAG-ASN         : angle       7.71742 (    3)
  link_BETA1-4         : bond        0.01057 (    2)
  link_BETA1-4         : angle       2.77218 (    6)
  hydrogen bonds       : bond        0.03930 (  214)
  hydrogen bonds       : angle       6.34759 (  612)
  SS BOND              : bond        0.00260 (   11)
  SS BOND              : angle       1.39607 (   22)
  covalent geometry    : bond        0.00431 ( 6764)
  covalent geometry    : angle       0.62445 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8034 (ptt)
REVERT: B   95 ARG cc_start: 0.5110 (mmt180) cc_final: 0.3683 (tmm160)
  outliers start: 11
  outliers final: 6
  residues processed: 102
  average time/residue: 1.9826
  time to fit residues: 216.5114
Evaluate side-chains
  102 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  281 ASN
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 56 optimal weight:    0.1980
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.139312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.121409 restraints weight = 27976.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 2.41
r_work: 0.3572 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6778  Z= 0.149
  Angle     :  0.618   8.775   9234  Z= 0.310
  Chirality :  0.044   0.171    997
  Planarity :  0.004   0.044   1193
  Dihedral  :  5.841  59.116    994
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 13.06 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.92 (0.29), residues: 827
  helix:  0.71 (0.37), residues: 192
  sheet: -1.61 (0.42), residues: 129
  loop : -0.84 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 932 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.021   0.002   PHE A 737 
 TYR   0.009   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01166 (    1)
  link_NAG-ASN         : angle       7.44752 (    3)
  link_BETA1-4         : bond        0.00847 (    2)
  link_BETA1-4         : angle       2.33382 (    6)
  hydrogen bonds       : bond        0.03679 (  214)
  hydrogen bonds       : angle       6.19290 (  612)
  SS BOND              : bond        0.00197 (   11)
  SS BOND              : angle       1.11203 (   22)
  covalent geometry    : bond        0.00328 ( 6764)
  covalent geometry    : angle       0.59912 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 LYS cc_start: 0.8071 (ptmm) cc_final: 0.7816 (pttm)
  outliers start: 10
  outliers final: 6
  residues processed: 102
  average time/residue: 1.8292
  time to fit residues: 200.6841
Evaluate side-chains
  100 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.137036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.119125 restraints weight = 27959.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.40
r_work: 0.3545 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   6778  Z= 0.224
  Angle     :  0.668   9.128   9234  Z= 0.336
  Chirality :  0.046   0.197    997
  Planarity :  0.005   0.046   1193
  Dihedral  :  6.103  58.724    994
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 13.34 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.99 (0.29), residues: 827
  helix:  0.69 (0.37), residues: 186
  sheet: -1.64 (0.42), residues: 129
  loop : -0.89 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 498 
 HIS   0.005   0.001   HIS A 582 
 PHE   0.018   0.002   PHE A 638 
 TYR   0.012   0.002   TYR A 774 
 ARG   0.004   0.001   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00599 (    1)
  link_NAG-ASN         : angle       7.94489 (    3)
  link_BETA1-4         : bond        0.01336 (    2)
  link_BETA1-4         : angle       2.84339 (    6)
  hydrogen bonds       : bond        0.04011 (  214)
  hydrogen bonds       : angle       6.27479 (  612)
  SS BOND              : bond        0.00252 (   11)
  SS BOND              : angle       1.33493 (   22)
  covalent geometry    : bond        0.00500 ( 6764)
  covalent geometry    : angle       0.64619 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7830 (ptt)
REVERT: A  465 LYS cc_start: 0.8138 (ptmm) cc_final: 0.7863 (pttm)
REVERT: B   95 ARG cc_start: 0.5131 (tpt-90) cc_final: 0.4265 (ppt90)
  outliers start: 11
  outliers final: 7
  residues processed: 104
  average time/residue: 1.9610
  time to fit residues: 219.0260
Evaluate side-chains
  107 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain A residue  920 LYS
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 78 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 766 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.138792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.121092 restraints weight = 27909.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.36
r_work: 0.3562 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6778  Z= 0.172
  Angle     :  0.637   8.721   9234  Z= 0.319
  Chirality :  0.045   0.183    997
  Planarity :  0.005   0.044   1193
  Dihedral  :  5.935  59.121    994
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.90 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.93 (0.29), residues: 827
  helix:  0.81 (0.38), residues: 186
  sheet: -1.64 (0.42), residues: 129
  loop : -0.86 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 861 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.020   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00905 (    1)
  link_NAG-ASN         : angle       7.43513 (    3)
  link_BETA1-4         : bond        0.00945 (    2)
  link_BETA1-4         : angle       2.40453 (    6)
  hydrogen bonds       : bond        0.03756 (  214)
  hydrogen bonds       : angle       6.19150 (  612)
  SS BOND              : bond        0.00214 (   11)
  SS BOND              : angle       1.08923 (   22)
  covalent geometry    : bond        0.00383 ( 6764)
  covalent geometry    : angle       0.61811 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7809 (ptt)
REVERT: A  465 LYS cc_start: 0.8114 (ptmm) cc_final: 0.7839 (pttm)
REVERT: B   95 ARG cc_start: 0.5088 (tpt-90) cc_final: 0.4002 (ttp-170)
  outliers start: 15
  outliers final: 9
  residues processed: 111
  average time/residue: 1.9669
  time to fit residues: 234.3842
Evaluate side-chains
  109 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain A residue  920 LYS
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 46 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 70 optimal weight:    0.4980
   overall best weight:    0.4156

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.139551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.121779 restraints weight = 27805.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.40
r_work: 0.3582 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6778  Z= 0.141
  Angle     :  0.624   8.383   9234  Z= 0.313
  Chirality :  0.044   0.166    997
  Planarity :  0.004   0.044   1193
  Dihedral  :  5.667  56.060    994
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.04 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.82 (0.29), residues: 827
  helix:  1.00 (0.38), residues: 186
  sheet: -1.57 (0.43), residues: 129
  loop : -0.84 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 932 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.011   0.001   PHE A 638 
 TYR   0.009   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01026 (    1)
  link_NAG-ASN         : angle       6.97111 (    3)
  link_BETA1-4         : bond        0.00683 (    2)
  link_BETA1-4         : angle       2.11323 (    6)
  hydrogen bonds       : bond        0.03550 (  214)
  hydrogen bonds       : angle       6.06031 (  612)
  SS BOND              : bond        0.00343 (   11)
  SS BOND              : angle       0.93034 (   22)
  covalent geometry    : bond        0.00319 ( 6764)
  covalent geometry    : angle       0.60775 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7730 (ptt)
REVERT: A  465 LYS cc_start: 0.8078 (ptmm) cc_final: 0.7793 (pttm)
REVERT: B   95 ARG cc_start: 0.5049 (tpt-90) cc_final: 0.4040 (ttp-170)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 1.9171
  time to fit residues: 215.9785
Evaluate side-chains
  106 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain A residue  920 LYS
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN
A 886 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.137708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.119965 restraints weight = 27919.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.39
r_work: 0.3558 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3454 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6778  Z= 0.201
  Angle     :  0.658   8.709   9234  Z= 0.331
  Chirality :  0.045   0.189    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  5.782  54.994    994
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.47 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.91 (0.29), residues: 827
  helix:  0.85 (0.38), residues: 186
  sheet: -1.59 (0.42), residues: 129
  loop : -0.88 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 932 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.019   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00408 (    1)
  link_NAG-ASN         : angle       6.88220 (    3)
  link_BETA1-4         : bond        0.01150 (    2)
  link_BETA1-4         : angle       2.47659 (    6)
  hydrogen bonds       : bond        0.03797 (  214)
  hydrogen bonds       : angle       6.14144 (  612)
  SS BOND              : bond        0.00274 (   11)
  SS BOND              : angle       1.15034 (   22)
  covalent geometry    : bond        0.00451 ( 6764)
  covalent geometry    : angle       0.64124 ( 9203)

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

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

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1654 Ramachandran restraints generated.
    827 Oldfield, 0 Emsley, 827 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7822 (ptt)
REVERT: A  465 LYS cc_start: 0.8147 (ptmm) cc_final: 0.7878 (pttm)
  outliers start: 10
  outliers final: 9
  residues processed: 107
  average time/residue: 1.9561
  time to fit residues: 224.3837
Evaluate side-chains
  110 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  232 LYS
Chi-restraints excluded: chain A residue  375 MET
Chi-restraints excluded: chain A residue  502 SER
Chi-restraints excluded: chain A residue  515 ASN
Chi-restraints excluded: chain A residue  550 SER
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  660 ASN
Chi-restraints excluded: chain A residue  920 LYS
Chi-restraints excluded: chain B residue  177 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 236 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.138352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.120723 restraints weight = 27904.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.38
r_work: 0.3568 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3463 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6778  Z= 0.171
  Angle     :  0.632   8.741   9234  Z= 0.322
  Chirality :  0.044   0.181    997
  Planarity :  0.004   0.044   1193
  Dihedral  :  5.508  44.195    994
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.61 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 17.65 %
    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: -0.87 (0.29), residues: 827
  helix:  0.91 (0.38), residues: 187
  sheet: -1.56 (0.43), residues: 129
  loop : -0.87 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 932 
 HIS   0.004   0.001   HIS A 463 
 PHE   0.013   0.002   PHE A 638 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.004   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    1)
  link_NAG-ASN         : angle       3.57822 (    3)
  link_BETA1-4         : bond        0.00970 (    2)
  link_BETA1-4         : angle       2.17547 (    6)
  hydrogen bonds       : bond        0.03670 (  214)
  hydrogen bonds       : angle       6.07385 (  612)
  SS BOND              : bond        0.00194 (   11)
  SS BOND              : angle       1.02308 (   22)
  covalent geometry    : bond        0.00384 ( 6764)
  covalent geometry    : angle       0.62554 ( 9203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10728.44 seconds
wall clock time: 185 minutes 20.14 seconds (11120.14 seconds total)