Starting phenix.real_space_refine
on Sun May 11 05:05:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/05_2025/9coo_45787.cif"
  }
  resolution = 3.73
  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=   0.006
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: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      36      5.16       5
     C    4685      2.51       5
     N    1266      2.21       5
     O    1503      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 7493
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3170
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 11, 'TRANS': 411}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 162
          Unresolved non-hydrogen angles: 196
          Unresolved non-hydrogen dihedrals: 155
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 101
    Chain: "B"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 926
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 6, 'TRANS': 121}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 54
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "H"
      Number of atoms: 923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 923
          Classifications: {'peptide': 125}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 6, 'TRANS': 118}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "L"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 769
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 57
          Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "N"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 859
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 67
    Chain: "R"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 801
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 112
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 94
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 91
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          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: "R"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.06, per 1000 atoms: 0.68
  Number of scatterers: 7493
  At special positions: 0
  Unit cell: (104.58, 117.86, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      36     16.00
     O    1503      8.00
     N    1266      7.00
     C    4685      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  68 " - pdb=" SG  CYS R  82 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  75 " - pdb=" SG  CYS R  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  89 " - pdb=" SG  CYS R 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 109 " - pdb=" SG  CYS R 121 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 128 " - pdb=" SG  CYS R 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 148 " - pdb=" SG  CYS R 160 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 155 " - pdb=" SG  CYS R 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 167 " - pdb=" SG  CYS R 184 " 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
    NAG-ASN
      " NAG A4601 " - " ASN A3336 "
      " NAG A4602 " - " ASN A3101 "
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1890

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 11 sheets defined
      13.0% alpha, 30.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'B' and resid 335 through 353
      removed outlier: 4.163A  pdb=" N   ALA B 339 " --> pdb=" O   PRO B 335 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   TYR B 342 " --> pdb=" O   SER B 338 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ILE B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 370
      removed outlier: 3.783A  pdb=" N   ALA B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   MET B 370 " --> pdb=" O   GLN B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 388
    Processing helix  chain 'B' and resid 391 through 406
      removed outlier: 3.612A  pdb=" N   GLU B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 428
      removed outlier: 4.077A  pdb=" N   SER B 422 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU B 428 " --> pdb=" O   PHE B 424 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 448
    Processing helix  chain 'B' and resid 451 through 469
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.937A  pdb=" N   LEU L  89 " --> pdb=" O   PRO L  86 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.756A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 86 through 88
      No H-bonds generated for 'chain 'R' and resid 86 through 88'
    Processing helix  chain 'R' and resid 137 through 142
      removed outlier: 3.855A  pdb=" N   SER R 142 " --> pdb=" O   SER R 138 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 184 through 189
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2825 through 2831
      removed outlier: 3.570A  pdb=" N   VAL A2828 " --> pdb=" O   HIS A2839 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   HIS A2839 " --> pdb=" O   VAL A2828 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A2846 " --> pdb=" O   ALA A2849 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA A2849 " --> pdb=" O   PHE A2846 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A2858 " --> pdb=" O   LEU A2869 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   THR A2866 " --> pdb=" O   LYS A2892 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU A2868 " --> pdb=" O   PHE A2890 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   PHE A2890 " --> pdb=" O   GLU A2868 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A2906 " --> pdb=" O   TYR A2889 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE A2895 " --> pdb=" O   PHE A2900 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2918 through 2922
    current: chain 'A' and resid 2939 through 2951
      removed outlier: 3.649A  pdb=" N   ASN A2961 " --> pdb=" O   GLN A2972 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 2968 through 2975
    current: chain 'A' and resid 3000 through 3009
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 3015 through 3023
    current: chain 'A' and resid 3030 through 3031
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 3030 through 3031
    current: chain 'A' and resid 3064 through 3074
      removed outlier: 4.172A  pdb=" N   ASP A3069 " --> pdb=" O   ARG A3092 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG A3092 " --> pdb=" O   ASP A3069 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   SER A3090 " --> pdb=" O   LEU A3071 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   TYR A3098 " --> pdb=" O   ALA A3091 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR A3096 " --> pdb=" O   PHE A3093 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 3337 through 3344
      removed outlier: 3.669A  pdb=" N   ALA A3364 " --> pdb=" O   THR A3385 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A3385 " --> pdb=" O   ALA A3364 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A3366 " --> pdb=" O   GLY A3383 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY A3383 " --> pdb=" O   LEU A3366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 46 through 51
      removed outlier: 4.836A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA6, first strand: chain 'L' and resid 39 through 44
      removed outlier: 6.306A  pdb=" N   LEU L  39 " --> pdb=" O   TYR L  55 " (cutoff:3.500A)
      removed outlier: 4.559A  pdb=" N   TYR L  55 " --> pdb=" O   LEU L  39 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'L' and resid 59 through 60
    current: chain 'L' and resid 102 through 103
    Processing sheet with id=AA7, first strand: chain 'N' and resid 6 through 7
      removed outlier: 3.549A  pdb=" N   SER N  71 " --> pdb=" O   TYR N  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 13
      removed outlier: 6.434A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 120 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   SER N 122 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   VAL N  12 " --> pdb=" O   SER N 122 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   MET N  34 " --> pdb=" O   ILE N  51 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 74
    Processing sheet with id=AB1, first strand: chain 'R' and resid 113 through 115
    Processing sheet with id=AB2, first strand: chain 'R' and resid 152 through 154
      removed outlier: 3.590A  pdb=" N   ILE R 161 " --> pdb=" O   PHE R 153 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    759 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: 2.20

  Time building geometry restraints manager: 2.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2471
        1.34 -     1.46: 1309
        1.46 -     1.57: 3811
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 7638
  Sorted by residual:
  bond pdb=" CB  ASP L  66 "
       pdb=" CG  ASP L  66 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.30e+00
  bond pdb=" CB  ASN B 379 "
       pdb=" CG  ASN B 379 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.14e+00
  bond pdb=" CB  GLU A2826 "
       pdb=" CG  GLU A2826 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.73e-01
  bond pdb=" CB  CYS H  96 "
       pdb=" SG  CYS H  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.775  0.033 3.30e-02 9.18e+02 9.73e-01
  bond pdb=" CA  ASN H  77 "
       pdb=" CB  ASN H  77 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.015 1.61e-02 3.86e+03 9.17e-01
  ... (remaining 7633 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10183
        1.92 -     3.84: 185
        3.84 -     5.75: 25
        5.75 -     7.67: 11
        7.67 -     9.59: 4
  Bond angle restraints: 10408
  Sorted by residual:
  angle pdb=" CA  ARG B 345 "
        pdb=" CB  ARG B 345 "
        pdb=" CG  ARG B 345 "
      ideal   model   delta    sigma   weight residual
     114.10  121.08   -6.98 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" C2  NAG A4602 "
        pdb=" N2  NAG A4602 "
        pdb=" C7  NAG A4602 "
      ideal   model   delta    sigma   weight residual
     124.56  133.57   -9.01 3.00e+00 1.11e-01 9.03e+00
  angle pdb=" CB  ARG B 345 "
        pdb=" CG  ARG B 345 "
        pdb=" CD  ARG B 345 "
      ideal   model   delta    sigma   weight residual
     111.30  118.00   -6.70 2.30e+00 1.89e-01 8.49e+00
  angle pdb=" CA  LEU A2869 "
        pdb=" CB  LEU A2869 "
        pdb=" CG  LEU A2869 "
      ideal   model   delta    sigma   weight residual
     116.30  125.89   -9.59 3.50e+00 8.16e-02 7.51e+00
  angle pdb=" CB  MET A3007 "
        pdb=" CG  MET A3007 "
        pdb=" SD  MET A3007 "
      ideal   model   delta    sigma   weight residual
     112.70  120.87   -8.17 3.00e+00 1.11e-01 7.41e+00
  ... (remaining 10403 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3870
       16.47 -    32.93: 485
       32.93 -    49.40: 145
       49.40 -    65.87: 41
       65.87 -    82.34: 5
  Dihedral angle restraints: 4546
    sinusoidal: 1606
      harmonic: 2940
  Sorted by residual:
  dihedral pdb=" CB  CYS R 155 "
           pdb=" SG  CYS R 155 "
           pdb=" SG  CYS R 173 "
           pdb=" CB  CYS R 173 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.19   57.19     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CB  CYS R 109 "
           pdb=" SG  CYS R 109 "
           pdb=" SG  CYS R 121 "
           pdb=" CB  CYS R 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.47   56.47     1      1.00e+01 1.00e-02 4.30e+01
  dihedral pdb=" CB  CYS R  68 "
           pdb=" SG  CYS R  68 "
           pdb=" SG  CYS R  82 "
           pdb=" CB  CYS R  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.80  -53.80     1      1.00e+01 1.00e-02 3.93e+01
  ... (remaining 4543 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1017
       0.056 -    0.112: 160
       0.112 -    0.168: 25
       0.168 -    0.224: 0
       0.224 -    0.279: 2
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" C1  NAG A4602 "
            pdb=" ND2 ASN A3101 "
            pdb=" C2  NAG A4602 "
            pdb=" O5  NAG A4602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CG  LEU B 462 "
            pdb=" CB  LEU B 462 "
            pdb=" CD1 LEU B 462 "
            pdb=" CD2 LEU B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" C2  NAG A4602 "
            pdb=" C1  NAG A4602 "
            pdb=" C3  NAG A4602 "
            pdb=" N2  NAG A4602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 1201 not shown)

  Planarity restraints: 1359
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A2971 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   ASN A2971 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASN A2971 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A2972 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R  83 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.20e+00
        pdb=" N   PRO R  84 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R  84 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R  84 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A2895 "    0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A2896 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A2896 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A2896 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1356 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 577
        2.73 -     3.27: 8002
        3.27 -     3.81: 12364
        3.81 -     4.36: 14118
        4.36 -     4.90: 24213
  Nonbonded interactions: 59274
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 448 "
            pdb=" ND2 ASN B 454 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OD1 ASP R 170 "
            pdb="CA    CA R 903 "
     model   vdw
     2.226 2.510
  nonbonded pdb=" OE2 GLU R 101 "
            pdb="CA    CA R 901 "
     model   vdw
     2.233 2.510
  nonbonded pdb=" O   SER R 130 "
            pdb=" OG  SER R 130 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   TYR A3379 "
            pdb=" NZ  LYS A3380 "
     model   vdw
     2.236 3.120
  ... (remaining 59269 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.700
  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:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.370
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7652  Z= 0.155
  Angle     :  0.677  11.241  10438  Z= 0.337
  Chirality :  0.043   0.279   1204
  Planarity :  0.004   0.051   1357
  Dihedral  : 16.582  82.337   2620
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 32.36 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.26), residues: 1006
  helix: -0.50 (0.46), residues: 123
  sheet: -1.96 (0.24), residues: 441
  loop : -1.69 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  87 
 HIS   0.011   0.001   HIS N 104 
 PHE   0.015   0.001   PHE A3038 
 TYR   0.016   0.001   TYR B 342 
 ARG   0.003   0.000   ARG A2836 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01162 (    2)
  link_NAG-ASN         : angle       5.55840 (    6)
  hydrogen bonds       : bond        0.14111 (  278)
  hydrogen bonds       : angle       8.13022 (  759)
  SS BOND              : bond        0.00229 (   12)
  SS BOND              : angle       1.03109 (   24)
  covalent geometry    : bond        0.00342 ( 7638)
  covalent geometry    : angle       0.66309 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7825 (tmm) cc_final: 0.6856 (tmm)
REVERT: A 3174 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7628 (mtpt)
REVERT: A 3340 ASP cc_start: 0.7895 (p0) cc_final: 0.7523 (m-30)
REVERT: B  456 LEU cc_start: 0.8882 (tp) cc_final: 0.8604 (tt)
REVERT: H   29 PHE cc_start: 0.8251 (t80) cc_final: 0.7677 (t80)
REVERT: H  108 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7257 (m-80)
REVERT: L   79 LEU cc_start: 0.7855 (tp) cc_final: 0.7254 (pp)
  outliers start: 11
  outliers final: 7
  residues processed: 109
  average time/residue: 0.1758
  time to fit residues: 26.9811
Evaluate side-chains
  106 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   84 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.2980
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.111858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.099728 restraints weight = 23025.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099801 restraints weight = 16053.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.100457 restraints weight = 14804.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.0945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7652  Z= 0.221
  Angle     :  0.690  12.422  10438  Z= 0.348
  Chirality :  0.044   0.324   1204
  Planarity :  0.005   0.048   1357
  Dihedral  :  5.905  53.570   1146
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.65 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 28.14 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.26), residues: 1006
  helix:  0.31 (0.49), residues: 121
  sheet: -1.98 (0.25), residues: 427
  loop : -1.70 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R 165 
 HIS   0.011   0.001   HIS N 104 
 PHE   0.017   0.002   PHE B 424 
 TYR   0.016   0.002   TYR A3177 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01111 (    2)
  link_NAG-ASN         : angle       6.20181 (    6)
  hydrogen bonds       : bond        0.03772 (  278)
  hydrogen bonds       : angle       6.47889 (  759)
  SS BOND              : bond        0.00238 (   12)
  SS BOND              : angle       0.83053 (   24)
  covalent geometry    : bond        0.00485 ( 7638)
  covalent geometry    : angle       0.67364 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 97
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7790 (tmm) cc_final: 0.7032 (tmm)
REVERT: A 2933 CYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6175 (m)
REVERT: A 3106 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.7776 (m-40)
REVERT: A 3174 LYS cc_start: 0.7684 (mmtm) cc_final: 0.7401 (mtpt)
REVERT: B  426 GLU cc_start: 0.7056 (pp20) cc_final: 0.6678 (pp20)
REVERT: B  456 LEU cc_start: 0.8579 (tp) cc_final: 0.8168 (tt)
REVERT: H  108 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6952 (m-80)
REVERT: R  168 ASP cc_start: 0.7566 (m-30) cc_final: 0.6952 (p0)
  outliers start: 40
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1678
  time to fit residues: 29.9043
Evaluate side-chains
  114 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3021 HIS
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   97 TYR
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 79 optimal weight:    0.5980
   chunk 90 optimal weight:    0.3980
   chunk 85 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A2839 HIS
A3353 ASN
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.112881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099200 restraints weight = 23420.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100822 restraints weight = 14148.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.101883 restraints weight = 10015.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7652  Z= 0.163
  Angle     :  0.648  12.485  10438  Z= 0.319
  Chirality :  0.043   0.310   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.764  54.259   1146
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 28.14 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.27), residues: 1006
  helix:  0.65 (0.50), residues: 121
  sheet: -1.92 (0.25), residues: 424
  loop : -1.62 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.017   0.001   PHE B 424 
 TYR   0.016   0.001   TYR A3177 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01317 (    2)
  link_NAG-ASN         : angle       6.27984 (    6)
  hydrogen bonds       : bond        0.03188 (  278)
  hydrogen bonds       : angle       6.12168 (  759)
  SS BOND              : bond        0.00271 (   12)
  SS BOND              : angle       0.65055 (   24)
  covalent geometry    : bond        0.00358 ( 7638)
  covalent geometry    : angle       0.63067 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7984 (tmm) cc_final: 0.7260 (tmm)
REVERT: A 2933 CYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6164 (m)
REVERT: A 3166 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8241 (tptp)
REVERT: B  360 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6433 (tt0)
REVERT: B  426 GLU cc_start: 0.7043 (pp20) cc_final: 0.6675 (pp20)
REVERT: B  456 LEU cc_start: 0.8652 (tp) cc_final: 0.8425 (mt)
REVERT: B  464 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7853 (mp0)
REVERT: H  108 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6912 (m-80)
  outliers start: 38
  outliers final: 26
  residues processed: 129
  average time/residue: 0.1891
  time to fit residues: 33.5558
Evaluate side-chains
  123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3097 LYS
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A2848 ASN
A3353 ASN
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.108942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.095508 restraints weight = 23373.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.096974 restraints weight = 14652.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.097913 restraints weight = 10665.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   7652  Z= 0.337
  Angle     :  0.798  12.500  10438  Z= 0.408
  Chirality :  0.046   0.313   1204
  Planarity :  0.005   0.051   1357
  Dihedral  :  6.618  54.507   1145
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 27.08 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.26), residues: 1006
  helix:  0.17 (0.49), residues: 114
  sheet: -2.24 (0.24), residues: 441
  loop : -1.87 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP H  47 
 HIS   0.010   0.002   HIS N 104 
 PHE   0.016   0.002   PHE A3038 
 TYR   0.024   0.003   TYR L  55 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00877 (    2)
  link_NAG-ASN         : angle       6.25427 (    6)
  hydrogen bonds       : bond        0.04036 (  278)
  hydrogen bonds       : angle       6.70269 (  759)
  SS BOND              : bond        0.00309 (   12)
  SS BOND              : angle       0.88468 (   24)
  covalent geometry    : bond        0.00731 ( 7638)
  covalent geometry    : angle       0.78377 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 92
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7978 (tmm) cc_final: 0.7279 (tmm)
REVERT: A 2933 CYS cc_start: 0.6555 (OUTLIER) cc_final: 0.5727 (m)
REVERT: A 3106 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7901 (m-40)
REVERT: A 3166 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (tptp)
REVERT: A 3359 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.4641 (pm20)
REVERT: B  360 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6678 (tt0)
REVERT: B  426 GLU cc_start: 0.7260 (pp20) cc_final: 0.7015 (pp20)
REVERT: B  464 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7834 (mp0)
REVERT: H   79 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8437 (tp)
REVERT: H  108 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.6865 (m-80)
REVERT: L   55 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8452 (p90)
  outliers start: 58
  outliers final: 36
  residues processed: 139
  average time/residue: 0.1842
  time to fit residues: 35.0844
Evaluate side-chains
  130 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 85
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 2997 VAL
Chi-restraints excluded: chain A residue 3021 HIS
Chi-restraints excluded: chain A residue 3097 LYS
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3363 VAL
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue   79 LEU
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   55 TYR
Chi-restraints excluded: chain L residue   97 TYR
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0770
   chunk 60 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 82 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 64 optimal weight:    0.1980
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:    0.2980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.112811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099410 restraints weight = 23121.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.100998 restraints weight = 13951.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.102043 restraints weight = 9897.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7652  Z= 0.136
  Angle     :  0.647  12.828  10438  Z= 0.319
  Chirality :  0.044   0.293   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.950  53.856   1145
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 28.27 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.26), residues: 1006
  helix:  0.74 (0.52), residues: 116
  sheet: -2.03 (0.25), residues: 419
  loop : -1.67 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.011   0.001   PHE B 424 
 TYR   0.021   0.001   TYR A2889 
 ARG   0.005   0.000   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01363 (    2)
  link_NAG-ASN         : angle       6.44478 (    6)
  hydrogen bonds       : bond        0.03020 (  278)
  hydrogen bonds       : angle       6.07233 (  759)
  SS BOND              : bond        0.00220 (   12)
  SS BOND              : angle       0.77317 (   24)
  covalent geometry    : bond        0.00300 ( 7638)
  covalent geometry    : angle       0.62807 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 100
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2822 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7127 (mm)
REVERT: A 2843 MET cc_start: 0.8054 (tmm) cc_final: 0.7345 (tmm)
REVERT: A 2933 CYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6746 (m)
REVERT: B  360 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6590 (tt0)
REVERT: B  456 LEU cc_start: 0.8646 (tp) cc_final: 0.8441 (mt)
REVERT: B  464 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7667 (mp0)
REVERT: H   76 LYS cc_start: 0.7276 (pttp) cc_final: 0.7040 (pttp)
REVERT: H  108 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6787 (m-80)
REVERT: N    5 GLN cc_start: 0.4664 (OUTLIER) cc_final: 0.4192 (pm20)
  outliers start: 45
  outliers final: 28
  residues processed: 137
  average time/residue: 0.1908
  time to fit residues: 35.5669
Evaluate side-chains
  124 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3097 LYS
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0870
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0770
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
** A3099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.112193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.098567 restraints weight = 23190.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.100206 restraints weight = 13918.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.101270 restraints weight = 9848.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7652  Z= 0.173
  Angle     :  0.668  12.554  10438  Z= 0.333
  Chirality :  0.043   0.286   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.907  57.401   1144
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  6.34 %
    Allowed  : 29.06 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.26), residues: 1006
  helix:  0.78 (0.53), residues: 117
  sheet: -2.09 (0.25), residues: 426
  loop : -1.58 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R 165 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.018   0.002   PHE B 340 
 TYR   0.022   0.002   TYR B 342 
 ARG   0.003   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01152 (    2)
  link_NAG-ASN         : angle       6.36614 (    6)
  hydrogen bonds       : bond        0.03102 (  278)
  hydrogen bonds       : angle       6.04007 (  759)
  SS BOND              : bond        0.00241 (   12)
  SS BOND              : angle       0.66115 (   24)
  covalent geometry    : bond        0.00385 ( 7638)
  covalent geometry    : angle       0.65098 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 93
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8061 (tmm) cc_final: 0.7294 (tmm)
REVERT: A 2933 CYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6029 (m)
REVERT: A 3359 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.4603 (pm20)
REVERT: B  360 GLN cc_start: 0.6901 (OUTLIER) cc_final: 0.6600 (tt0)
REVERT: B  464 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7808 (mp0)
REVERT: H  108 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6872 (m-80)
  outliers start: 48
  outliers final: 40
  residues processed: 132
  average time/residue: 0.1819
  time to fit residues: 33.1979
Evaluate side-chains
  131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 86
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0670
   chunk 79 optimal weight:    0.0970
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A3094 ASN
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.114003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.100547 restraints weight = 23170.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.102137 restraints weight = 14009.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.103189 restraints weight = 9931.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7652  Z= 0.125
  Angle     :  0.638  12.589  10438  Z= 0.314
  Chirality :  0.043   0.277   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.572  54.612   1144
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.19 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 1006
  helix:  0.97 (0.54), residues: 117
  sheet: -1.87 (0.25), residues: 418
  loop : -1.54 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.010   0.001   PHE B 424 
 TYR   0.016   0.001   TYR A3177 
 ARG   0.003   0.000   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01291 (    2)
  link_NAG-ASN         : angle       6.36271 (    6)
  hydrogen bonds       : bond        0.02812 (  278)
  hydrogen bonds       : angle       5.79186 (  759)
  SS BOND              : bond        0.00206 (   12)
  SS BOND              : angle       0.56477 (   24)
  covalent geometry    : bond        0.00283 ( 7638)
  covalent geometry    : angle       0.61979 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2822 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7171 (mm)
REVERT: A 2843 MET cc_start: 0.8053 (tmm) cc_final: 0.7376 (tmm)
REVERT: A 2844 LEU cc_start: 0.7343 (mm) cc_final: 0.7082 (mp)
REVERT: A 2933 CYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6717 (m)
REVERT: B  360 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6549 (tt0)
REVERT: B  456 LEU cc_start: 0.8545 (mt) cc_final: 0.8338 (mt)
REVERT: H  108 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6858 (m-80)
REVERT: L    3 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6538 (mmp)
REVERT: N    5 GLN cc_start: 0.5430 (OUTLIER) cc_final: 0.4808 (pm20)
REVERT: N   38 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8027 (ttp-170)
  outliers start: 43
  outliers final: 32
  residues processed: 134
  average time/residue: 0.1716
  time to fit residues: 32.0747
Evaluate side-chains
  132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3099 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    3 MET
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.112084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.098620 restraints weight = 23447.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.100157 restraints weight = 14266.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.101135 restraints weight = 10237.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7652  Z= 0.193
  Angle     :  0.688  12.398  10438  Z= 0.343
  Chirality :  0.043   0.280   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.775  55.225   1144
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 28.53 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.27), residues: 1006
  helix:  0.78 (0.51), residues: 121
  sheet: -1.97 (0.25), residues: 426
  loop : -1.54 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.017   0.002   PHE A3038 
 TYR   0.027   0.002   TYR B 342 
 ARG   0.003   0.001   ARG N  67 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01106 (    2)
  link_NAG-ASN         : angle       6.28096 (    6)
  hydrogen bonds       : bond        0.03091 (  278)
  hydrogen bonds       : angle       5.93960 (  759)
  SS BOND              : bond        0.00242 (   12)
  SS BOND              : angle       0.85636 (   24)
  covalent geometry    : bond        0.00429 ( 7638)
  covalent geometry    : angle       0.67075 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 96
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8051 (tmm) cc_final: 0.7328 (tmm)
REVERT: A 2933 CYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5954 (m)
REVERT: A 3174 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8621 (ttmt)
REVERT: A 3359 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.4586 (pm20)
REVERT: B  360 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6542 (tt0)
REVERT: B  464 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7835 (mp0)
REVERT: H   29 PHE cc_start: 0.8070 (t80) cc_final: 0.7720 (t80)
REVERT: H  108 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6758 (m-80)
  outliers start: 51
  outliers final: 40
  residues processed: 137
  average time/residue: 0.1700
  time to fit residues: 32.8513
Evaluate side-chains
  138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 92
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3174 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 7 optimal weight:    0.2980
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.111557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.097966 restraints weight = 23624.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.099602 restraints weight = 14085.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100627 restraints weight = 9894.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
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      :  0.004   0.052   7652  Z= 0.197
  Angle     :  0.700  12.459  10438  Z= 0.349
  Chirality :  0.044   0.283   1204
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.862  55.574   1144
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 28.80 %
    Favored  : 64.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.27), residues: 1006
  helix:  0.81 (0.51), residues: 121
  sheet: -1.89 (0.25), residues: 429
  loop : -1.58 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP R 165 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.016   0.002   PHE B 340 
 TYR   0.017   0.002   TYR L  55 
 ARG   0.003   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01162 (    2)
  link_NAG-ASN         : angle       6.28606 (    6)
  hydrogen bonds       : bond        0.03143 (  278)
  hydrogen bonds       : angle       5.99993 (  759)
  SS BOND              : bond        0.00254 (   12)
  SS BOND              : angle       0.78678 (   24)
  covalent geometry    : bond        0.00439 ( 7638)
  covalent geometry    : angle       0.68305 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 93
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8052 (tmm) cc_final: 0.7376 (tmm)
REVERT: A 2933 CYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6906 (m)
REVERT: A 3174 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8592 (ttmt)
REVERT: A 3359 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.4602 (pm20)
REVERT: B  360 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6617 (tt0)
REVERT: B  464 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7833 (mp0)
REVERT: H   29 PHE cc_start: 0.8096 (t80) cc_final: 0.7725 (t80)
REVERT: H  108 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6902 (m-80)
  outliers start: 50
  outliers final: 42
  residues processed: 134
  average time/residue: 0.1852
  time to fit residues: 34.2174
Evaluate side-chains
  140 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 92
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3174 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3359 GLN
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0370
   chunk 45 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.112512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.099005 restraints weight = 23493.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100630 restraints weight = 14138.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101705 restraints weight = 9950.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7652  Z= 0.164
  Angle     :  0.692  12.495  10438  Z= 0.342
  Chirality :  0.043   0.285   1204
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.716  55.345   1144
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 29.46 %
    Favored  : 63.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.14 (0.27), residues: 1006
  helix:  0.83 (0.52), residues: 122
  sheet: -1.84 (0.26), residues: 419
  loop : -1.49 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP R 165 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.019   0.002   PHE A3038 
 TYR   0.029   0.002   TYR B 342 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01236 (    2)
  link_NAG-ASN         : angle       6.32127 (    6)
  hydrogen bonds       : bond        0.02963 (  278)
  hydrogen bonds       : angle       5.90006 (  759)
  SS BOND              : bond        0.00209 (   12)
  SS BOND              : angle       0.74539 (   24)
  covalent geometry    : bond        0.00369 ( 7638)
  covalent geometry    : angle       0.67478 (10408)

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 98
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8048 (tmm) cc_final: 0.7388 (tmm)
REVERT: A 2844 LEU cc_start: 0.7396 (mm) cc_final: 0.7125 (mp)
REVERT: A 2933 CYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6888 (m)
REVERT: A 3174 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8585 (ttmt)
REVERT: B  360 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6627 (tt0)
REVERT: B  464 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7814 (mp0)
REVERT: H   29 PHE cc_start: 0.8100 (t80) cc_final: 0.7849 (t80)
REVERT: H  108 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6732 (m-80)
REVERT: L   79 LEU cc_start: 0.7734 (tp) cc_final: 0.7041 (pp)
REVERT: N    5 GLN cc_start: 0.5573 (OUTLIER) cc_final: 0.4930 (pm20)
REVERT: N   38 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8017 (ttp-170)
  outliers start: 50
  outliers final: 43
  residues processed: 137
  average time/residue: 0.1735
  time to fit residues: 33.2726
Evaluate side-chains
  141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 91
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3173 VAL
Chi-restraints excluded: chain A residue 3174 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.112271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.098885 restraints weight = 23374.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.100455 restraints weight = 14160.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.101510 restraints weight = 10018.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7652  Z= 0.163
  Angle     :  0.682  13.747  10438  Z= 0.338
  Chirality :  0.043   0.259   1204
  Planarity :  0.004   0.051   1357
  Dihedral  :  5.734  55.460   1144
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 29.19 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.11 (0.27), residues: 1006
  helix:  0.92 (0.52), residues: 121
  sheet: -1.81 (0.26), residues: 418
  loop : -1.50 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP R 165 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.017   0.001   PHE B 340 
 TYR   0.022   0.002   TYR A2889 
 ARG   0.008   0.001   ARG A3389 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01092 (    2)
  link_NAG-ASN         : angle       6.64300 (    6)
  hydrogen bonds       : bond        0.02913 (  278)
  hydrogen bonds       : angle       5.82932 (  759)
  SS BOND              : bond        0.00200 (   12)
  SS BOND              : angle       0.72784 (   24)
  covalent geometry    : bond        0.00365 ( 7638)
  covalent geometry    : angle       0.66275 (10408)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2744.28 seconds
wall clock time: 48 minutes 42.71 seconds (2922.71 seconds total)