Starting phenix.real_space_refine
on Thu Jul 31 07:05:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uw8_42639/07_2025/8uw8_42639_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uw8_42639/07_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_42639/07_2025/8uw8_42639.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uw8_42639/07_2025/8uw8_42639.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uw8_42639/07_2025/8uw8_42639_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uw8_42639/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.35, per 1000 atoms: 0.79
  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: 4.36
  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: 1.34
  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: 5.36

  Time building geometry restraints manager: 4.58 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:             27.130
  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:             0.220
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     36.930
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:13.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   78.600
-------------------------------------------------------------------------------
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  : 0.964 
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: 2.2051
  time to fit residues: 347.2824
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  : 0.960 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.4342

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.140756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.122696 restraints weight = 27551.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3663 rms_B_bonded: 2.39
r_work: 0.3579 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6778  Z= 0.153
  Angle     :  0.642   8.718   9234  Z= 0.323
  Chirality :  0.045   0.181    997
  Planarity :  0.005   0.043   1193
  Dihedral  :  8.078  60.972    994
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.41 %
    Favored  : 89.47 %
  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:  0.62 (0.36), residues: 192
  sheet: -1.58 (0.43), residues: 129
  loop : -0.76 (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   0.017   0.002   PHE A 737 
 TYR   0.012   0.001   TYR A 869 
 ARG   0.009   0.001   ARG A 840 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01102 (    1)
  link_NAG-ASN         : angle       7.18283 (    3)
  link_BETA1-4         : bond        0.01087 (    2)
  link_BETA1-4         : angle       3.13046 (    6)
  hydrogen bonds       : bond        0.04350 (  214)
  hydrogen bonds       : angle       6.85693 (  612)
  SS BOND              : bond        0.00309 (   11)
  SS BOND              : angle       1.09135 (   22)
  covalent geometry    : bond        0.00336 ( 6764)
  covalent geometry    : angle       0.62240 ( 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
  121 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.032 
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
  outliers start: 8
  outliers final: 2
  residues processed: 115
  average time/residue: 1.8572
  time to fit residues: 230.4394
Evaluate side-chains
  102 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 LYS
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:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.139236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.121333 restraints weight = 27917.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.40
r_work: 0.3565 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.1771

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= 0.173
  Angle     :  0.631   8.981   9234  Z= 0.318
  Chirality :  0.045   0.180    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  6.507  56.573    994
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 10.53 %
    Favored  : 88.62 %
  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: -0.94 (0.29), residues: 827
  helix:  0.58 (0.36), residues: 191
  sheet: -1.53 (0.42), residues: 131
  loop : -0.82 (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   0.014   0.002   PHE A 638 
 TYR   0.012   0.001   TYR A 774 
 ARG   0.004   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01040 (    1)
  link_NAG-ASN         : angle       7.59833 (    3)
  link_BETA1-4         : bond        0.01024 (    2)
  link_BETA1-4         : angle       2.95458 (    6)
  hydrogen bonds       : bond        0.04165 (  214)
  hydrogen bonds       : angle       6.51027 (  612)
  SS BOND              : bond        0.00288 (   11)
  SS BOND              : angle       1.09053 (   22)
  covalent geometry    : bond        0.00381 ( 6764)
  covalent geometry    : angle       0.60981 ( 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
  111 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 1.029 
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: 0.8047 (mtp)
REVERT: B   80 GLN cc_start: 0.5884 (tm-30) cc_final: 0.5671 (tm130)
  outliers start: 6
  outliers final: 4
  residues processed: 107
  average time/residue: 1.8401
  time to fit residues: 212.3984
Evaluate side-chains
  98 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 54 optimal weight:    0.4980
   chunk 34 optimal weight:    0.2980
   chunk 78 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
B 181 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.139164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.121345 restraints weight = 27778.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3652 rms_B_bonded: 2.39
r_work: 0.3569 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3462 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6778  Z= 0.162
  Angle     :  0.620   8.898   9234  Z= 0.312
  Chirality :  0.045   0.177    997
  Planarity :  0.004   0.044   1193
  Dihedral  :  6.000  57.645    994
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  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:  0.67 (0.37), residues: 191
  sheet: -1.55 (0.42), residues: 129
  loop : -0.83 (0.28), residues: 507

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        0.01156 (    1)
  link_NAG-ASN         : angle       7.46009 (    3)
  link_BETA1-4         : bond        0.00841 (    2)
  link_BETA1-4         : angle       2.64594 (    6)
  hydrogen bonds       : bond        0.03906 (  214)
  hydrogen bonds       : angle       6.36679 (  612)
  SS BOND              : bond        0.00229 (   11)
  SS BOND              : angle       0.99642 (   22)
  covalent geometry    : bond        0.00357 ( 6764)
  covalent geometry    : angle       0.60084 ( 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
  112 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.964 
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: 0.8404 (ttp) cc_final: 0.8059 (mtp)
  outliers start: 7
  outliers final: 5
  residues processed: 107
  average time/residue: 1.8570
  time to fit residues: 213.8323
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  : 1.050 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN
B 181 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.137786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.120027 restraints weight = 28195.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.40
r_work: 0.3536 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6778  Z= 0.199
  Angle     :  0.653   9.045   9234  Z= 0.327
  Chirality :  0.045   0.188    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  6.009  57.875    994
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 12.36 %
    Favored  : 86.38 %
  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: -0.98 (0.29), residues: 827
  helix:  0.57 (0.37), residues: 192
  sheet: -1.59 (0.42), residues: 129
  loop : -0.85 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 498 
 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   0.004   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00892 (    1)
  link_NAG-ASN         : angle       7.72454 (    3)
  link_BETA1-4         : bond        0.01139 (    2)
  link_BETA1-4         : angle       2.77037 (    6)
  hydrogen bonds       : bond        0.03945 (  214)
  hydrogen bonds       : angle       6.33477 (  612)
  SS BOND              : bond        0.00305 (   11)
  SS BOND              : angle       1.77570 (   22)
  covalent geometry    : bond        0.00441 ( 6764)
  covalent geometry    : angle       0.62920 ( 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
  108 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8001 (ptt)
REVERT: A  465 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7779 (pttm)
REVERT: B   95 ARG cc_start: 0.5123 (mmt180) cc_final: 0.3666 (tmm160)
  outliers start: 9
  outliers final: 4
  residues processed: 102
  average time/residue: 2.0497
  time to fit residues: 223.8834
Evaluate side-chains
  100 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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  660 ASN
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:    0.2980
   chunk 13 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.138168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.120297 restraints weight = 28228.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.41
r_work: 0.3554 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3446 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2130

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= 0.181
  Angle     :  0.638   8.945   9234  Z= 0.320
  Chirality :  0.045   0.182    997
  Planarity :  0.004   0.044   1193
  Dihedral  :  5.930  58.897    994
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 13.34 %
    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: -0.97 (0.29), residues: 827
  helix:  0.61 (0.37), residues: 192
  sheet: -1.61 (0.42), residues: 129
  loop : -0.86 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 498 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.023   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.002   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00960 (    1)
  link_NAG-ASN         : angle       7.64964 (    3)
  link_BETA1-4         : bond        0.01006 (    2)
  link_BETA1-4         : angle       2.54556 (    6)
  hydrogen bonds       : bond        0.03850 (  214)
  hydrogen bonds       : angle       6.24854 (  612)
  SS BOND              : bond        0.00258 (   11)
  SS BOND              : angle       1.50731 (   22)
  covalent geometry    : bond        0.00400 ( 6764)
  covalent geometry    : angle       0.61632 ( 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: 8
    poor density    : 100
  time to evaluate  : 0.979 
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: 0.8116 (ptmm) cc_final: 0.7850 (pttm)
REVERT: B   95 ARG cc_start: 0.5107 (mmt180) cc_final: 0.3740 (tmm160)
  outliers start: 8
  outliers final: 6
  residues processed: 104
  average time/residue: 2.0489
  time to fit residues: 228.3439
Evaluate side-chains
  102 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.137316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.119565 restraints weight = 28050.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.39
r_work: 0.3550 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6778  Z= 0.199
  Angle     :  0.656   8.954   9234  Z= 0.329
  Chirality :  0.045   0.187    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  5.964  59.198    994
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.62 %
    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: -1.00 (0.29), residues: 827
  helix:  0.60 (0.37), residues: 192
  sheet: -1.63 (0.42), residues: 129
  loop : -0.88 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 498 
 HIS   0.004   0.001   HIS A 582 
 PHE   0.015   0.002   PHE A 638 
 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        0.00816 (    1)
  link_NAG-ASN         : angle       7.73308 (    3)
  link_BETA1-4         : bond        0.01106 (    2)
  link_BETA1-4         : angle       2.61530 (    6)
  hydrogen bonds       : bond        0.03900 (  214)
  hydrogen bonds       : angle       6.23574 (  612)
  SS BOND              : bond        0.00295 (   11)
  SS BOND              : angle       1.37423 (   22)
  covalent geometry    : bond        0.00443 ( 6764)
  covalent geometry    : angle       0.63486 ( 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
  106 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 1.006 
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: 0.8665 (OUTLIER) cc_final: 0.8015 (ptt)
REVERT: A  465 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7796 (pttm)
REVERT: B   95 ARG cc_start: 0.5134 (mmt180) cc_final: 0.3770 (tmm160)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 2.4503
  time to fit residues: 263.6558
Evaluate side-chains
  105 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
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 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:    0.0970
   chunk 78 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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
A 766 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 = 0.138264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.120503 restraints weight = 28032.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.39
r_work: 0.3562 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6778  Z= 0.162
  Angle     :  0.627   8.638   9234  Z= 0.314
  Chirality :  0.045   0.177    997
  Planarity :  0.005   0.044   1193
  Dihedral  :  5.801  58.996    994
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.34 %
    Favored  : 84.97 %
  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:  0.86 (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 861 
 HIS   0.003   0.001   HIS A 582 
 PHE   0.019   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.006   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00968 (    1)
  link_NAG-ASN         : angle       7.42787 (    3)
  link_BETA1-4         : bond        0.00876 (    2)
  link_BETA1-4         : angle       2.34394 (    6)
  hydrogen bonds       : bond        0.03704 (  214)
  hydrogen bonds       : angle       6.14227 (  612)
  SS BOND              : bond        0.00222 (   11)
  SS BOND              : angle       1.16065 (   22)
  covalent geometry    : bond        0.00360 ( 6764)
  covalent geometry    : angle       0.60793 ( 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
  113 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 1.187 
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: 0.8656 (OUTLIER) cc_final: 0.7996 (ptt)
REVERT: A  465 LYS cc_start: 0.8069 (ptmm) cc_final: 0.7784 (pttm)
REVERT: B   95 ARG cc_start: 0.5088 (mmt180) cc_final: 0.3794 (tmm160)
  outliers start: 12
  outliers final: 7
  residues processed: 107
  average time/residue: 2.6400
  time to fit residues: 303.4266
Evaluate side-chains
  104 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 2.220 
-------------------------------------------------------------------------------
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 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:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 13 optimal weight:    0.2980
   chunk 46 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0050
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.140035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.122482 restraints weight = 27942.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.38
r_work: 0.3591 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6778  Z= 0.129
  Angle     :  0.619   8.226   9234  Z= 0.310
  Chirality :  0.044   0.159    997
  Planarity :  0.004   0.043   1193
  Dihedral  :  5.511  56.268    994
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.76 %
    Favored  : 84.41 %
  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: -0.75 (0.30), residues: 827
  helix:  1.05 (0.38), residues: 186
  sheet: -1.48 (0.43), residues: 129
  loop : -0.81 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 861 
 HIS   0.002   0.001   HIS A 582 
 PHE   0.010   0.001   PHE A 638 
 TYR   0.008   0.001   TYR A 774 
 ARG   0.005   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01147 (    1)
  link_NAG-ASN         : angle       6.99665 (    3)
  link_BETA1-4         : bond        0.00651 (    2)
  link_BETA1-4         : angle       2.01907 (    6)
  hydrogen bonds       : bond        0.03482 (  214)
  hydrogen bonds       : angle       6.01360 (  612)
  SS BOND              : bond        0.00178 (   11)
  SS BOND              : angle       0.97444 (   22)
  covalent geometry    : bond        0.00293 ( 6764)
  covalent geometry    : angle       0.60260 ( 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
  115 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.940 
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: 0.8074 (ptmm) cc_final: 0.7806 (pttm)
REVERT: B   95 ARG cc_start: 0.5103 (mmt180) cc_final: 0.3828 (tmm160)
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 1.9974
  time to fit residues: 227.6747
Evaluate side-chains
  105 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3850 r_free = 0.3850 target = 0.137423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.119664 restraints weight = 28109.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.39
r_work: 0.3551 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6778  Z= 0.205
  Angle     :  0.664   8.723   9234  Z= 0.334
  Chirality :  0.045   0.191    997
  Planarity :  0.005   0.045   1193
  Dihedral  :  5.739  56.228    994
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.19 %
    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: -0.87 (0.29), residues: 827
  helix:  0.89 (0.38), residues: 186
  sheet: -1.55 (0.42), residues: 129
  loop : -0.86 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 498 
 HIS   0.005   0.001   HIS A 582 
 PHE   0.019   0.002   PHE A 737 
 TYR   0.010   0.001   TYR A 774 
 ARG   0.007   0.000   ARG A 451 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       7.20723 (    3)
  link_BETA1-4         : bond        0.00992 (    2)
  link_BETA1-4         : angle       2.57524 (    6)
  hydrogen bonds       : bond        0.03833 (  214)
  hydrogen bonds       : angle       6.12145 (  612)
  SS BOND              : bond        0.00270 (   11)
  SS BOND              : angle       1.28966 (   22)
  covalent geometry    : bond        0.00460 ( 6764)
  covalent geometry    : angle       0.64588 ( 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
  116 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.967 
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  375 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8019 (ptt)
REVERT: A  465 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7869 (pttm)
  outliers start: 13
  outliers final: 9
  residues processed: 108
  average time/residue: 2.0978
  time to fit residues: 243.0027
Evaluate side-chains
  111 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 68 optimal weight:    0.2980
   chunk 58 optimal weight:    0.4980
   chunk 72 optimal weight:    0.0030
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.3190

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.140370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.122798 restraints weight = 27905.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 2.38
r_work: 0.3596 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3490 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6778  Z= 0.127
  Angle     :  0.619   8.917   9234  Z= 0.311
  Chirality :  0.045   0.195    997
  Planarity :  0.004   0.042   1193
  Dihedral  :  5.290  49.277    994
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.17 %
    Favored  : 83.57 %
  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: -0.72 (0.30), residues: 827
  helix:  1.10 (0.39), residues: 187
  sheet: -1.43 (0.43), residues: 139
  loop : -0.79 (0.29), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 861 
 HIS   0.002   0.001   HIS A 225 
 PHE   0.010   0.001   PHE A 682 
 TYR   0.009   0.001   TYR A 774 
 ARG   0.006   0.000   ARG B  95 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00691 (    1)
  link_NAG-ASN         : angle       5.15594 (    3)
  link_BETA1-4         : bond        0.00569 (    2)
  link_BETA1-4         : angle       1.85005 (    6)
  hydrogen bonds       : bond        0.03446 (  214)
  hydrogen bonds       : angle       5.96410 (  612)
  SS BOND              : bond        0.00175 (   11)
  SS BOND              : angle       0.92534 (   22)
  covalent geometry    : bond        0.00292 ( 6764)
  covalent geometry    : angle       0.60947 ( 9203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12067.17 seconds
wall clock time: 210 minutes 42.53 seconds (12642.53 seconds total)