Starting phenix.real_space_refine
on Fri Jun  6 09:25:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/06_2025/9coo_45787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/06_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_45787/06_2025/9coo_45787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/06_2025/9coo_45787.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9coo_45787/06_2025/9coo_45787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/06_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-5710/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: 5.49, per 1000 atoms: 0.73
  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: 2.04
  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: 0.89
  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: 2.15

  Time building geometry restraints manager: 2.40 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:             2.330
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.000
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.750
-------------------------------------------------------------------------------
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  : 0.820 
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: 0.1709
  time to fit residues: 26.2256
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  : 0.919 
-------------------------------------------------------------------------------
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 = 0.111859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.099714 restraints weight = 23071.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.099771 restraints weight = 16139.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.100462 restraints weight = 14796.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.0941

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     :  0.689  12.411  10438  Z= 0.347
  Chirality :  0.044   0.325   1204
  Planarity :  0.005   0.048   1357
  Dihedral  :  5.903  53.567   1146
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 28.40 %
    Favored  : 66.45 %
  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        0.01116 (    2)
  link_NAG-ASN         : angle       6.20228 (    6)
  hydrogen bonds       : bond        0.03765 (  278)
  hydrogen bonds       : angle       6.47804 (  759)
  SS BOND              : bond        0.00245 (   12)
  SS BOND              : angle       0.82579 (   24)
  covalent geometry    : bond        0.00485 ( 7638)
  covalent geometry    : angle       0.67261 (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
  135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 96
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7790 (tmm) cc_final: 0.7029 (tmm)
REVERT: A 2933 CYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6186 (m)
REVERT: A 3106 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.7768 (m-40)
REVERT: A 3174 LYS cc_start: 0.7691 (mmtm) cc_final: 0.7406 (mtpt)
REVERT: B  426 GLU cc_start: 0.7063 (pp20) cc_final: 0.6687 (pp20)
REVERT: B  456 LEU cc_start: 0.8583 (tp) cc_final: 0.8173 (tt)
REVERT: H  108 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.6952 (m-80)
REVERT: R  168 ASP cc_start: 0.7574 (m-30) cc_final: 0.6959 (p0)
  outliers start: 39
  outliers final: 21
  residues processed: 126
  average time/residue: 0.1683
  time to fit residues: 29.7864
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  : 0.807 
-------------------------------------------------------------------------------
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:    0.0270
   chunk 90 optimal weight:    0.3980
   chunk 85 optimal weight:    0.2980
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0980
   chunk 48 optimal weight:    0.0980
   overall best weight:    0.1838

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

Flipped N/Q/H residues before XYZ refinement:
A2839 HIS
** A2865 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.115367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101823 restraints weight = 23229.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.103434 restraints weight = 13742.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.104494 restraints weight = 9702.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7652  Z= 0.111
  Angle     :  0.618  12.528  10438  Z= 0.301
  Chirality :  0.043   0.306   1204
  Planarity :  0.004   0.047   1357
  Dihedral  :  5.498  53.820   1146
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 28.14 %
    Favored  : 67.77 %
  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: -2.21 (0.27), residues: 1006
  helix:  0.65 (0.51), residues: 122
  sheet: -1.77 (0.25), residues: 422
  loop : -1.61 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 165 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.017   0.001   PHE B 424 
 TYR   0.015   0.001   TYR A3177 
 ARG   0.004   0.000   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01442 (    2)
  link_NAG-ASN         : angle       6.30422 (    6)
  hydrogen bonds       : bond        0.02994 (  278)
  hydrogen bonds       : angle       5.91932 (  759)
  SS BOND              : bond        0.00315 (   12)
  SS BOND              : angle       0.56712 (   24)
  covalent geometry    : bond        0.00242 ( 7638)
  covalent geometry    : angle       0.59962 (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
  140 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 0.903 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7960 (tmm) cc_final: 0.7280 (tmm)
REVERT: A 2844 LEU cc_start: 0.7138 (mm) cc_final: 0.6897 (mp)
REVERT: A 2933 CYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6170 (m)
REVERT: A 3166 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8151 (tptt)
REVERT: B  341 TRP cc_start: 0.7403 (m100) cc_final: 0.7189 (m100)
REVERT: B  360 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6383 (tt0)
REVERT: B  456 LEU cc_start: 0.8584 (tp) cc_final: 0.8367 (mt)
REVERT: B  464 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7726 (mp0)
REVERT: H  108 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6718 (m-80)
  outliers start: 31
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1719
  time to fit residues: 31.8496
Evaluate side-chains
  115 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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 2963 ILE
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0470
   chunk 65 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.5680

-------------------------------------------------------------------------------
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 = 0.4085 r_free = 0.4085 target = 0.113439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.099925 restraints weight = 23143.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.101541 restraints weight = 14011.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.102546 restraints weight = 9919.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1379

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= 0.169
  Angle     :  0.648  12.437  10438  Z= 0.322
  Chirality :  0.043   0.287   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.694  54.772   1146
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.01 %
    Favored  : 67.24 %
  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 (0.26), residues: 1006
  helix:  0.69 (0.51), residues: 121
  sheet: -1.83 (0.25), residues: 422
  loop : -1.63 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 165 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.017   0.002   PHE B 424 
 TYR   0.020   0.002   TYR A2889 
 ARG   0.003   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01226 (    2)
  link_NAG-ASN         : angle       6.22562 (    6)
  hydrogen bonds       : bond        0.03056 (  278)
  hydrogen bonds       : angle       5.92027 (  759)
  SS BOND              : bond        0.00235 (   12)
  SS BOND              : angle       0.76038 (   24)
  covalent geometry    : bond        0.00373 ( 7638)
  covalent geometry    : angle       0.63062 (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
  130 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7975 (tmm) cc_final: 0.7224 (tmm)
REVERT: A 2844 LEU cc_start: 0.7284 (mm) cc_final: 0.7032 (mp)
REVERT: A 2933 CYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6159 (m)
REVERT: A 3166 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8220 (tptp)
REVERT: B  360 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6451 (tt0)
REVERT: B  456 LEU cc_start: 0.8627 (tp) cc_final: 0.8421 (mt)
REVERT: B  464 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7771 (mp0)
REVERT: H  108 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6909 (m-80)
REVERT: N   65 LYS cc_start: 0.8601 (tppt) cc_final: 0.8309 (tppt)
  outliers start: 36
  outliers final: 26
  residues processed: 120
  average time/residue: 0.1662
  time to fit residues: 28.2762
Evaluate side-chains
  122 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
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  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   25 SER
Chi-restraints excluded: chain N residue   32 VAL
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  107 LEU
Chi-restraints excluded: chain R residue   94 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    0.3980
   chunk 82 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.112324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.098737 restraints weight = 23052.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.100374 restraints weight = 13746.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.101461 restraints weight = 9665.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1593

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= 0.191
  Angle     :  0.661  12.323  10438  Z= 0.330
  Chirality :  0.044   0.292   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.872  55.002   1146
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 27.61 %
    Favored  : 66.71 %
  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: -2.24 (0.27), residues: 1006
  helix:  0.76 (0.53), residues: 116
  sheet: -1.84 (0.25), residues: 422
  loop : -1.59 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N 113 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.017   0.001   PHE B 424 
 TYR   0.019   0.002   TYR A2889 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01131 (    2)
  link_NAG-ASN         : angle       6.21183 (    6)
  hydrogen bonds       : bond        0.03133 (  278)
  hydrogen bonds       : angle       6.00558 (  759)
  SS BOND              : bond        0.00242 (   12)
  SS BOND              : angle       0.81398 (   24)
  covalent geometry    : bond        0.00422 ( 7638)
  covalent geometry    : angle       0.64359 (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
  142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 99
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8067 (tmm) cc_final: 0.7445 (tmm)
REVERT: A 2933 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6082 (m)
REVERT: A 3166 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8215 (tptp)
REVERT: B  341 TRP cc_start: 0.7171 (m100) cc_final: 0.6913 (m100)
REVERT: B  360 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6497 (tt0)
REVERT: B  426 GLU cc_start: 0.6842 (pp20) cc_final: 0.6578 (pp20)
REVERT: B  464 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7718 (mp0)
REVERT: H  108 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6857 (m-80)
  outliers start: 43
  outliers final: 32
  residues processed: 132
  average time/residue: 0.1829
  time to fit residues: 33.3543
Evaluate side-chains
  124 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 87
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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 2898 LEU
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 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 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   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   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
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:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4045 r_free = 0.4045 target = 0.111367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.099205 restraints weight = 23236.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.099423 restraints weight = 15940.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.099741 restraints weight = 13860.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7652  Z= 0.218
  Angle     :  0.687  12.269  10438  Z= 0.345
  Chirality :  0.044   0.294   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  6.086  55.290   1146
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  7.40 %
    Allowed  : 27.34 %
    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: -2.36 (0.27), residues: 1006
  helix:  0.66 (0.52), residues: 117
  sheet: -1.98 (0.25), residues: 437
  loop : -1.57 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.016   0.002   PHE A3038 
 TYR   0.023   0.002   TYR B 342 
 ARG   0.002   0.000   ARG H  99 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01141 (    2)
  link_NAG-ASN         : angle       6.18505 (    6)
  hydrogen bonds       : bond        0.03271 (  278)
  hydrogen bonds       : angle       6.11978 (  759)
  SS BOND              : bond        0.00294 (   12)
  SS BOND              : angle       0.86681 (   24)
  covalent geometry    : bond        0.00480 ( 7638)
  covalent geometry    : angle       0.67074 (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
  153 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 97
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8056 (tmm) cc_final: 0.7400 (tmm)
REVERT: A 2933 CYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6081 (m)
REVERT: A 3166 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8213 (tptp)
REVERT: A 3359 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.4621 (pm20)
REVERT: B  341 TRP cc_start: 0.7379 (m100) cc_final: 0.7129 (m100)
REVERT: B  360 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6640 (tt0)
REVERT: B  426 GLU cc_start: 0.6999 (pp20) cc_final: 0.6794 (pp20)
REVERT: B  464 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7904 (mp0)
REVERT: H   79 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (tp)
REVERT: H  108 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.6898 (m-80)
  outliers start: 56
  outliers final: 44
  residues processed: 139
  average time/residue: 0.1671
  time to fit residues: 32.7558
Evaluate side-chains
  139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 88
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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 2898 LEU
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 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 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 3359 GLN
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   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   37 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain L residue   97 TYR
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   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   94 ASP
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  136 ASP
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:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0570
   chunk 84 optimal weight:    0.4980
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
A3094 ASN
** A3114 HIS ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.113131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.099743 restraints weight = 23081.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.101348 restraints weight = 13879.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.102369 restraints weight = 9868.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1915

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= 0.135
  Angle     :  0.640  12.411  10438  Z= 0.316
  Chirality :  0.043   0.254   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.782  54.740   1146
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 28.67 %
    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: -2.14 (0.27), residues: 1006
  helix:  0.90 (0.53), residues: 117
  sheet: -1.84 (0.25), residues: 425
  loop : -1.47 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.010   0.001   HIS A3114 
 PHE   0.019   0.001   PHE B 424 
 TYR   0.014   0.001   TYR A3177 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01382 (    2)
  link_NAG-ASN         : angle       6.20144 (    6)
  hydrogen bonds       : bond        0.02894 (  278)
  hydrogen bonds       : angle       5.84598 (  759)
  SS BOND              : bond        0.00243 (   12)
  SS BOND              : angle       0.66005 (   24)
  covalent geometry    : bond        0.00302 ( 7638)
  covalent geometry    : angle       0.62261 (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
  143 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 97
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2822 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7178 (mm)
REVERT: A 2843 MET cc_start: 0.8027 (tmm) cc_final: 0.7504 (tmm)
REVERT: A 2933 CYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6729 (m)
REVERT: A 3166 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8072 (tptp)
REVERT: B  341 TRP cc_start: 0.7192 (m100) cc_final: 0.6947 (m100)
REVERT: B  360 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6517 (tt0)
REVERT: B  426 GLU cc_start: 0.6916 (pp20) cc_final: 0.6679 (pp20)
REVERT: B  462 LEU cc_start: 0.9012 (tp) cc_final: 0.8776 (tp)
REVERT: H  108 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6742 (m-80)
REVERT: N    5 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.5012 (pm20)
  outliers start: 46
  outliers final: 33
  residues processed: 134
  average time/residue: 0.1890
  time to fit residues: 35.0634
Evaluate side-chains
  129 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 90
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
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 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 3077 PHE
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 3173 VAL
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   26 THR
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   21 SER
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   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  123 SER
Chi-restraints excluded: chain R residue  135 LEU
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:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0040
   chunk 81 optimal weight:    0.0980
   chunk 13 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.2592

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 377 GLN
B 406 GLN
** 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 = 0.4102 r_free = 0.4102 target = 0.114392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.101045 restraints weight = 23252.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.102642 restraints weight = 13928.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.103676 restraints weight = 9857.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7652  Z= 0.118
  Angle     :  0.646  13.334  10438  Z= 0.319
  Chirality :  0.042   0.263   1204
  Planarity :  0.004   0.047   1357
  Dihedral  :  5.696  58.389   1145
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 29.85 %
    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: -2.03 (0.27), residues: 1006
  helix:  1.04 (0.52), residues: 121
  sheet: -1.75 (0.25), residues: 425
  loop : -1.45 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R  87 
 HIS   0.009   0.001   HIS N 104 
 PHE   0.021   0.001   PHE B 424 
 TYR   0.026   0.001   TYR B 342 
 ARG   0.005   0.000   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01318 (    2)
  link_NAG-ASN         : angle       6.55268 (    6)
  hydrogen bonds       : bond        0.02731 (  278)
  hydrogen bonds       : angle       5.66831 (  759)
  SS BOND              : bond        0.00242 (   12)
  SS BOND              : angle       0.85719 (   24)
  covalent geometry    : bond        0.00267 ( 7638)
  covalent geometry    : angle       0.62621 (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
  135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2822 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7266 (mm)
REVERT: A 2843 MET cc_start: 0.8003 (tmm) cc_final: 0.7531 (tmm)
REVERT: A 2933 CYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6737 (m)
REVERT: B  341 TRP cc_start: 0.7135 (m100) cc_final: 0.6903 (m100)
REVERT: B  360 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6647 (tt0)
REVERT: H  108 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6817 (m-80)
REVERT: L    3 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6530 (mmp)
REVERT: N    5 GLN cc_start: 0.5401 (OUTLIER) cc_final: 0.4905 (pm20)
REVERT: N   38 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8041 (ttp-170)
  outliers start: 38
  outliers final: 28
  residues processed: 127
  average time/residue: 0.1747
  time to fit residues: 31.0146
Evaluate side-chains
  123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 88
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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 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 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   26 THR
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 R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  135 LEU
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:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.111686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.098065 restraints weight = 23611.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.099709 restraints weight = 14138.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100767 restraints weight = 10008.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7652  Z= 0.212
  Angle     :  0.693  12.715  10438  Z= 0.349
  Chirality :  0.043   0.276   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  6.060  56.308   1145
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 29.06 %
    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: -2.16 (0.27), residues: 1006
  helix:  0.84 (0.53), residues: 117
  sheet: -1.85 (0.25), residues: 419
  loop : -1.48 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 
 PHE   0.019   0.002   PHE B 424 
 TYR   0.017   0.002   TYR A2889 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01105 (    2)
  link_NAG-ASN         : angle       6.29376 (    6)
  hydrogen bonds       : bond        0.03073 (  278)
  hydrogen bonds       : angle       5.91581 (  759)
  SS BOND              : bond        0.00267 (   12)
  SS BOND              : angle       0.83784 (   24)
  covalent geometry    : bond        0.00470 ( 7638)
  covalent geometry    : angle       0.67624 (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
  132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 89
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7997 (tmm) cc_final: 0.7391 (tmm)
REVERT: A 2933 CYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5991 (m)
REVERT: B  360 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6530 (tt0)
REVERT: B  426 GLU cc_start: 0.6700 (pp20) cc_final: 0.6488 (pp20)
REVERT: H  108 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6949 (m-80)
REVERT: L    3 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6609 (mmp)
REVERT: L   79 LEU cc_start: 0.7854 (tp) cc_final: 0.7041 (pp)
  outliers start: 43
  outliers final: 38
  residues processed: 122
  average time/residue: 0.1563
  time to fit residues: 27.6627
Evaluate side-chains
  128 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 86
  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 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 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  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   26 THR
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   93 TYR
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
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   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  135 LEU
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:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 45 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0670
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** 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 = 0.4069 r_free = 0.4069 target = 0.112704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099312 restraints weight = 23434.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.100883 restraints weight = 14124.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101860 restraints weight = 10074.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7652  Z= 0.165
  Angle     :  0.666  12.903  10438  Z= 0.332
  Chirality :  0.043   0.276   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.837  55.764   1145
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 29.06 %
    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: -2.13 (0.27), residues: 1006
  helix:  0.90 (0.51), residues: 122
  sheet: -1.87 (0.25), residues: 428
  loop : -1.44 (0.29), residues: 456

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   0.020   0.002   PHE B 424 
 TYR   0.021   0.002   TYR A2889 
 ARG   0.004   0.001   ARG A2836 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01224 (    2)
  link_NAG-ASN         : angle       6.33945 (    6)
  hydrogen bonds       : bond        0.02863 (  278)
  hydrogen bonds       : angle       5.78454 (  759)
  SS BOND              : bond        0.00239 (   12)
  SS BOND              : angle       0.79723 (   24)
  covalent geometry    : bond        0.00372 ( 7638)
  covalent geometry    : angle       0.64832 (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
  135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 91
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7981 (tmm) cc_final: 0.7471 (tmm)
REVERT: A 2933 CYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6868 (m)
REVERT: B  360 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6501 (tt0)
REVERT: B  426 GLU cc_start: 0.6975 (pp20) cc_final: 0.6727 (pp20)
REVERT: B  462 LEU cc_start: 0.8937 (tp) cc_final: 0.8737 (tp)
REVERT: H   79 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8303 (tp)
REVERT: H  108 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6753 (m-80)
REVERT: L    3 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6579 (mmp)
REVERT: L   79 LEU cc_start: 0.7737 (tp) cc_final: 0.7025 (pp)
REVERT: N    5 GLN cc_start: 0.5180 (OUTLIER) cc_final: 0.4684 (pm20)
REVERT: R  122 ILE cc_start: 0.8254 (mp) cc_final: 0.7852 (mm)
  outliers start: 44
  outliers final: 38
  residues processed: 124
  average time/residue: 0.1609
  time to fit residues: 29.2365
Evaluate side-chains
  133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 89
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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 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 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  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   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   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   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   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  130 SER
Chi-restraints excluded: chain R residue  135 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A3114 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.110951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.098804 restraints weight = 23419.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.099048 restraints weight = 16059.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.099372 restraints weight = 13844.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   7652  Z= 0.220
  Angle     :  0.706  12.622  10438  Z= 0.357
  Chirality :  0.044   0.272   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  6.076  55.181   1145
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 29.33 %
    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: -2.23 (0.27), residues: 1006
  helix:  0.82 (0.51), residues: 117
  sheet: -1.89 (0.25), residues: 431
  loop : -1.52 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP N 113 
 HIS   0.010   0.002   HIS N 104 
 PHE   0.018   0.002   PHE B 424 
 TYR   0.020   0.002   TYR A2889 
 ARG   0.004   0.001   ARG B 345 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00992 (    2)
  link_NAG-ASN         : angle       6.18004 (    6)
  hydrogen bonds       : bond        0.03130 (  278)
  hydrogen bonds       : angle       5.96757 (  759)
  SS BOND              : bond        0.00262 (   12)
  SS BOND              : angle       0.86836 (   24)
  covalent geometry    : bond        0.00490 ( 7638)
  covalent geometry    : angle       0.69052 (10408)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2735.06 seconds
wall clock time: 48 minutes 3.61 seconds (2883.61 seconds total)