Starting phenix.real_space_refine
on Wed Sep 17 09:09:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9coo_45787/09_2025/9coo_45787.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9coo_45787/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9coo_45787/09_2025/9coo_45787.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9coo_45787/09_2025/9coo_45787.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9coo_45787/09_2025/9coo_45787.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9coo_45787/09_2025/9coo_45787.map"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ARG:plan': 3, 'PHE:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2}
          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: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2}
          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, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 1}
          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, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 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: {'GLU:plan': 2, 'TYR:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 2}
          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: {'ASP:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 3, 'TRP:plan': 1}
          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: 1.85, per 1000 atoms: 0.25
  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: 0.55
  Conformation dependent library (CDL) restraints added in 382.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.26
  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: 1.12

  Time building geometry restraints manager: 0.72 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:             3.390
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.900
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
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 : 15.31
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG A2836 
 TYR   0.016   0.001   TYR B 342 
 PHE   0.015   0.001   PHE A3038 
 TRP   0.011   0.001   TRP R  87 
 HIS   0.011   0.001   HIS N 104 

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

*********************** 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  : 0.296 
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: 0.7255 (pp)
  outliers start: 11
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0724
  time to fit residues: 11.1510
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  : 0.285 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.112765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.099159 restraints weight = 23256.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.100752 restraints weight = 14087.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101766 restraints weight = 10043.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.102475 restraints weight = 7989.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.102827 restraints weight = 6838.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7652  Z= 0.194
  Angle     :  0.666  12.422  10438  Z= 0.335
  Chirality :  0.044   0.330   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.767  53.523   1146
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 29.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.42 (0.26), residues: 1006
  helix:  0.38 (0.49), residues: 121
  sheet: -1.92 (0.25), residues: 425
  loop : -1.70 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  99 
 TYR   0.016   0.002   TYR A3177 
 PHE   0.017   0.002   PHE B 424 
 TRP   0.028   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7638)
  covalent geometry    : angle       0.64943 (10408)
  SS BOND              : bond        0.00237 (   12)
  SS BOND              : angle       0.76333 (   24)
  hydrogen bonds       : bond        0.03680 (  278)
  hydrogen bonds       : angle       6.39775 (  759)
  link_NAG-ASN         : bond        0.01187 (    2)
  link_NAG-ASN         : angle       6.22877 (    6)

*********************** 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
  131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7742 (tmm) cc_final: 0.7056 (tmm)
REVERT: A 2933 CYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6032 (m)
REVERT: A 3106 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7840 (m-40)
REVERT: A 3126 LEU cc_start: 0.7686 (tp) cc_final: 0.7453 (tp)
REVERT: A 3174 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7437 (mtpt)
REVERT: B  456 LEU cc_start: 0.8597 (tp) cc_final: 0.8189 (tt)
REVERT: H  108 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6935 (m-80)
REVERT: R  168 ASP cc_start: 0.7789 (m-30) cc_final: 0.7060 (p0)
  outliers start: 32
  outliers final: 17
  residues processed: 123
  average time/residue: 0.0647
  time to fit residues: 11.3724
Evaluate side-chains
  112 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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 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 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 63 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 77 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.112377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.098721 restraints weight = 23232.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.100339 restraints weight = 14053.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.101380 restraints weight = 9967.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.102010 restraints weight = 7911.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.102492 restraints weight = 6820.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.1074

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= 0.188
  Angle     :  0.659  12.397  10438  Z= 0.328
  Chirality :  0.043   0.318   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.820  54.181   1146
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 27.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.41 (0.26), residues: 1006
  helix:  0.49 (0.50), residues: 121
  sheet: -1.96 (0.25), residues: 424
  loop : -1.66 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A3092 
 TYR   0.015   0.002   TYR A3177 
 PHE   0.014   0.002   PHE B 424 
 TRP   0.014   0.002   TRP R 165 
 HIS   0.010   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 7638)
  covalent geometry    : angle       0.64229 (10408)
  SS BOND              : bond        0.00249 (   12)
  SS BOND              : angle       0.66534 (   24)
  hydrogen bonds       : bond        0.03329 (  278)
  hydrogen bonds       : angle       6.21681 (  759)
  link_NAG-ASN         : bond        0.01230 (    2)
  link_NAG-ASN         : angle       6.24560 (    6)

*********************** 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: 44
    poor density    : 96
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A 2843 MET cc_start: 0.7965 (tmm) cc_final: 0.7248 (tmm)
REVERT: A 2933 CYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6196 (m)
REVERT: A 3106 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8108 (m-40)
REVERT: A 3166 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8270 (tptp)
REVERT: B  360 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6439 (tt0)
REVERT: B  426 GLU cc_start: 0.6692 (pp20) cc_final: 0.6413 (pp20)
REVERT: B  456 LEU cc_start: 0.8634 (tp) cc_final: 0.8412 (mt)
REVERT: B  464 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7858 (mp0)
REVERT: H  108 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6925 (m-80)
REVERT: R  168 ASP cc_start: 0.7605 (m-30) cc_final: 0.7098 (p0)
  outliers start: 44
  outliers final: 26
  residues processed: 131
  average time/residue: 0.0718
  time to fit residues: 13.1790
Evaluate side-chains
  125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 93
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 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  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   71 SER
Chi-restraints excluded: chain H residue  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   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
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0970
   chunk 92 optimal weight:    0.9990
   chunk 89 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0870
   chunk 75 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A2839 HIS
** 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 = 0.4096 r_free = 0.4096 target = 0.114174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100687 restraints weight = 23313.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.102320 restraints weight = 13801.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.103361 restraints weight = 9683.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.104049 restraints weight = 7660.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.104493 restraints weight = 6541.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7652  Z= 0.131
  Angle     :  0.621  12.761  10438  Z= 0.305
  Chirality :  0.043   0.285   1204
  Planarity :  0.004   0.047   1357
  Dihedral  :  5.586  54.550   1146
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.40 %
    Favored  : 67.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.27), residues: 1006
  helix:  0.72 (0.51), residues: 121
  sheet: -1.83 (0.25), residues: 424
  loop : -1.59 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 345 
 TYR   0.022   0.001   TYR A2889 
 PHE   0.018   0.001   PHE B 424 
 TRP   0.012   0.001   TRP R 165 
 HIS   0.009   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7638)
  covalent geometry    : angle       0.60203 (10408)
  SS BOND              : bond        0.00192 (   12)
  SS BOND              : angle       0.55803 (   24)
  hydrogen bonds       : bond        0.02930 (  278)
  hydrogen bonds       : angle       5.87880 (  759)
  link_NAG-ASN         : bond        0.01365 (    2)
  link_NAG-ASN         : angle       6.34146 (    6)

*********************** 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
  144 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A 2822 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7201 (mm)
REVERT: A 2843 MET cc_start: 0.7933 (tmm) cc_final: 0.7218 (tmm)
REVERT: A 2844 LEU cc_start: 0.7156 (mm) cc_final: 0.6887 (mp)
REVERT: A 2933 CYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6084 (m)
REVERT: A 3106 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8298 (m-40)
REVERT: A 3126 LEU cc_start: 0.7720 (tp) cc_final: 0.7425 (tp)
REVERT: A 3166 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8333 (tptp)
REVERT: B  456 LEU cc_start: 0.8634 (tp) cc_final: 0.8410 (mt)
REVERT: B  464 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7640 (mp0)
REVERT: H  108 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6727 (m-80)
REVERT: N   38 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7958 (ttp-170)
REVERT: N   65 LYS cc_start: 0.8575 (tppt) cc_final: 0.8331 (tppt)
  outliers start: 34
  outliers final: 22
  residues processed: 138
  average time/residue: 0.0738
  time to fit residues: 14.1829
Evaluate side-chains
  124 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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 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 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  367 ILE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue   26 THR
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 75 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A3099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4050 r_free = 0.4050 target = 0.111425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.099314 restraints weight = 23401.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.099153 restraints weight = 16501.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.099691 restraints weight = 15377.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.100047 restraints weight = 11776.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.100144 restraints weight = 10186.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7652  Z= 0.220
  Angle     :  0.678  12.385  10438  Z= 0.342
  Chirality :  0.044   0.275   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  6.000  54.985   1145
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 26.55 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.26), residues: 1006
  helix:  0.58 (0.52), residues: 116
  sheet: -1.96 (0.25), residues: 427
  loop : -1.59 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG N  67 
 TYR   0.017   0.002   TYR A3177 
 PHE   0.016   0.002   PHE B 424 
 TRP   0.014   0.002   TRP N 113 
 HIS   0.009   0.002   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 7638)
  covalent geometry    : angle       0.66111 (10408)
  SS BOND              : bond        0.00261 (   12)
  SS BOND              : angle       0.83800 (   24)
  hydrogen bonds       : bond        0.03256 (  278)
  hydrogen bonds       : angle       6.12316 (  759)
  link_NAG-ASN         : bond        0.01031 (    2)
  link_NAG-ASN         : angle       6.14611 (    6)

*********************** 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
  148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 98
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8090 (tmm) cc_final: 0.7424 (tmm)
REVERT: A 2933 CYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6018 (m)
REVERT: A 3106 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8058 (m-40)
REVERT: A 3166 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8261 (tptp)
REVERT: A 3359 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.4637 (pm20)
REVERT: B  341 TRP cc_start: 0.7332 (m100) cc_final: 0.7048 (m100)
REVERT: B  360 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6551 (tt0)
REVERT: B  426 GLU cc_start: 0.7097 (pp20) cc_final: 0.6809 (pp20)
REVERT: B  464 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7813 (mp0)
REVERT: H   76 LYS cc_start: 0.7725 (pttm) cc_final: 0.7452 (pttp)
REVERT: H   79 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8394 (tp)
REVERT: H  108 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6877 (m-80)
REVERT: N   65 LYS cc_start: 0.8658 (tppt) cc_final: 0.8353 (tppt)
  outliers start: 50
  outliers final: 36
  residues processed: 136
  average time/residue: 0.0809
  time to fit residues: 15.0942
Evaluate side-chains
  134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 90
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   52 LEU
Chi-restraints excluded: chain L residue   97 TYR
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   48 VAL
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   87 LYS
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 ** 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 = 0.4055 r_free = 0.4055 target = 0.111841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.098111 restraints weight = 23366.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.099779 restraints weight = 13973.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.100864 restraints weight = 9856.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.101526 restraints weight = 7781.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101864 restraints weight = 6681.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1867

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= 0.204
  Angle     :  0.682  12.520  10438  Z= 0.340
  Chirality :  0.044   0.272   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  6.055  54.850   1145
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 28.53 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.27), residues: 1006
  helix:  0.56 (0.51), residues: 117
  sheet: -2.00 (0.25), residues: 437
  loop : -1.56 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG N  67 
 TYR   0.023   0.002   TYR B 342 
 PHE   0.017   0.002   PHE B 424 
 TRP   0.014   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 7638)
  covalent geometry    : angle       0.66493 (10408)
  SS BOND              : bond        0.00259 (   12)
  SS BOND              : angle       0.69027 (   24)
  hydrogen bonds       : bond        0.03158 (  278)
  hydrogen bonds       : angle       6.09035 (  759)
  link_NAG-ASN         : bond        0.01143 (    2)
  link_NAG-ASN         : angle       6.31089 (    6)

*********************** 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
  148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 97
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8031 (tmm) cc_final: 0.7292 (tmm)
REVERT: A 2933 CYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5985 (m)
REVERT: A 3166 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8171 (tptp)
REVERT: A 3359 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.4604 (pm20)
REVERT: B  360 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6532 (tt0)
REVERT: B  426 GLU cc_start: 0.6775 (pp20) cc_final: 0.6564 (pp20)
REVERT: B  464 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7877 (mp0)
REVERT: H  108 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6730 (m-80)
  outliers start: 51
  outliers final: 39
  residues processed: 137
  average time/residue: 0.0817
  time to fit residues: 15.4968
Evaluate side-chains
  134 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 89
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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 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  427 ILE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    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 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   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
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    0.3980
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.112527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098859 restraints weight = 23347.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.100507 restraints weight = 13903.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.101609 restraints weight = 9841.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.102186 restraints weight = 7765.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.102690 restraints weight = 6744.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1940

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= 0.164
  Angle     :  0.657  12.628  10438  Z= 0.326
  Chirality :  0.043   0.267   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.966  54.736   1145
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 28.67 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.27), residues: 1006
  helix:  0.69 (0.52), residues: 117
  sheet: -1.95 (0.25), residues: 424
  loop : -1.52 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A2836 
 TYR   0.021   0.001   TYR A2889 
 PHE   0.020   0.002   PHE B 340 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.009   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7638)
  covalent geometry    : angle       0.63938 (10408)
  SS BOND              : bond        0.00221 (   12)
  SS BOND              : angle       0.62739 (   24)
  hydrogen bonds       : bond        0.03000 (  278)
  hydrogen bonds       : angle       5.98256 (  759)
  link_NAG-ASN         : bond        0.01197 (    2)
  link_NAG-ASN         : angle       6.35878 (    6)

*********************** 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
  151 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8011 (tmm) cc_final: 0.7445 (tmm)
REVERT: A 2933 CYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5956 (m)
REVERT: A 3106 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8138 (m-40)
REVERT: A 3166 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8124 (tptp)
REVERT: B  360 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6533 (tt0)
REVERT: B  426 GLU cc_start: 0.6885 (pp20) cc_final: 0.6605 (pp20)
REVERT: H  108 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6730 (m-80)
  outliers start: 50
  outliers final: 40
  residues processed: 143
  average time/residue: 0.0778
  time to fit residues: 15.5048
Evaluate side-chains
  135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 90
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  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   37 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   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 98 optimal weight:    0.4980
   chunk 79 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 ** 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 = 0.4064 r_free = 0.4064 target = 0.112345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.098687 restraints weight = 23533.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.100348 restraints weight = 14041.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.101423 restraints weight = 9886.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.102142 restraints weight = 7825.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.102482 restraints weight = 6662.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2069

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= 0.172
  Angle     :  0.676  12.648  10438  Z= 0.337
  Chirality :  0.043   0.261   1204
  Planarity :  0.004   0.051   1357
  Dihedral  :  6.032  57.620   1145
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 28.93 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.27), residues: 1006
  helix:  0.68 (0.51), residues: 122
  sheet: -1.88 (0.25), residues: 421
  loop : -1.49 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A3389 
 TYR   0.027   0.002   TYR B 342 
 PHE   0.018   0.002   PHE A3038 
 TRP   0.013   0.002   TRP N 113 
 HIS   0.009   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7638)
  covalent geometry    : angle       0.65836 (10408)
  SS BOND              : bond        0.00311 (   12)
  SS BOND              : angle       0.83123 (   24)
  hydrogen bonds       : bond        0.03094 (  278)
  hydrogen bonds       : angle       5.97255 (  759)
  link_NAG-ASN         : bond        0.01143 (    2)
  link_NAG-ASN         : angle       6.37327 (    6)

*********************** 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
  148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 98
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.8012 (tmm) cc_final: 0.7450 (tmm)
REVERT: A 2933 CYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5942 (m)
REVERT: A 3106 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8128 (m-40)
REVERT: A 3166 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8113 (tptp)
REVERT: B  360 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6532 (tt0)
REVERT: H   76 LYS cc_start: 0.8140 (pttp) cc_final: 0.7761 (pttm)
REVERT: H  108 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6763 (m-80)
  outliers start: 50
  outliers final: 45
  residues processed: 139
  average time/residue: 0.0694
  time to fit residues: 13.8672
Evaluate side-chains
  141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 91
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3353 ASN
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  108 TYR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain L residue    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 N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  114 PHE
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 46 optimal weight:    0.1980
   chunk 95 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0670
   chunk 43 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A3114 HIS
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.113001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.099398 restraints weight = 23231.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.101059 restraints weight = 13808.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.102142 restraints weight = 9701.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.102843 restraints weight = 7654.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.103147 restraints weight = 6542.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7652  Z= 0.155
  Angle     :  0.669  12.713  10438  Z= 0.333
  Chirality :  0.043   0.259   1204
  Planarity :  0.004   0.050   1357
  Dihedral  :  5.878  55.078   1145
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 29.85 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.27), residues: 1006
  helix:  0.80 (0.51), residues: 122
  sheet: -1.83 (0.25), residues: 421
  loop : -1.45 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A3389 
 TYR   0.019   0.001   TYR A3177 
 PHE   0.018   0.001   PHE B 340 
 TRP   0.013   0.001   TRP N 113 
 HIS   0.009   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7638)
  covalent geometry    : angle       0.65144 (10408)
  SS BOND              : bond        0.00230 (   12)
  SS BOND              : angle       0.74542 (   24)
  hydrogen bonds       : bond        0.03009 (  278)
  hydrogen bonds       : angle       5.88364 (  759)
  link_NAG-ASN         : bond        0.01194 (    2)
  link_NAG-ASN         : angle       6.40052 (    6)

*********************** 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
  146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 97
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7989 (tmm) cc_final: 0.7448 (tmm)
REVERT: A 2933 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6881 (m)
REVERT: A 3106 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8111 (m-40)
REVERT: A 3166 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8127 (tptp)
REVERT: B  360 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6524 (tt0)
REVERT: H   76 LYS cc_start: 0.8060 (pttp) cc_final: 0.7807 (pttm)
REVERT: H   79 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: H  108 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6754 (m-80)
REVERT: L    3 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6540 (mmp)
REVERT: N    5 GLN cc_start: 0.5113 (OUTLIER) cc_final: 0.4626 (pm20)
REVERT: N   38 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8071 (ttp-170)
  outliers start: 49
  outliers final: 40
  residues processed: 136
  average time/residue: 0.0666
  time to fit residues: 13.0611
Evaluate side-chains
  141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 92
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
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 3114 HIS
Chi-restraints excluded: chain A residue 3164 THR
Chi-restraints excluded: chain A residue 3166 LYS
Chi-restraints excluded: chain A residue 3355 GLU
Chi-restraints excluded: chain A residue 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   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 N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  136 ASP
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:    0.0670
   chunk 79 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A3114 HIS
** 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 = 0.4052 r_free = 0.4052 target = 0.111636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.097998 restraints weight = 23358.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.099630 restraints weight = 14139.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.100659 restraints weight = 9987.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.101404 restraints weight = 7900.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.101875 restraints weight = 6724.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2259

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= 0.200
  Angle     :  0.704  12.687  10438  Z= 0.352
  Chirality :  0.043   0.258   1204
  Planarity :  0.004   0.049   1357
  Dihedral  :  5.974  55.368   1145
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.95 %
    Favored  : 91.05 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 29.33 %
    Favored  : 63.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.27), residues: 1006
  helix:  0.80 (0.51), residues: 122
  sheet: -1.87 (0.25), residues: 433
  loop : -1.46 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A3389 
 TYR   0.030   0.002   TYR B 342 
 PHE   0.019   0.002   PHE A3038 
 TRP   0.018   0.002   TRP N 113 
 HIS   0.010   0.001   HIS N 104 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 ( 7638)
  covalent geometry    : angle       0.68776 (10408)
  SS BOND              : bond        0.00230 (   12)
  SS BOND              : angle       0.74737 (   24)
  hydrogen bonds       : bond        0.03207 (  278)
  hydrogen bonds       : angle       6.02443 (  759)
  link_NAG-ASN         : bond        0.00944 (    2)
  link_NAG-ASN         : angle       6.33413 (    6)

********************** 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
  145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A 2843 MET cc_start: 0.7982 (tmm) cc_final: 0.7426 (tmm)
REVERT: A 2933 CYS cc_start: 0.6656 (OUTLIER) cc_final: 0.5954 (m)
REVERT: A 3106 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8111 (m-40)
REVERT: A 3166 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8234 (tptp)
REVERT: B  360 GLN cc_start: 0.6927 (OUTLIER) cc_final: 0.6565 (tt0)
REVERT: B  464 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7805 (mp0)
REVERT: H   29 PHE cc_start: 0.8080 (t80) cc_final: 0.7698 (t80)
REVERT: H   79 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (tp)
REVERT: H  108 TYR cc_start: 0.7412 (OUTLIER) cc_final: 0.6773 (m-80)
REVERT: L    3 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6551 (mmp)
REVERT: L   79 LEU cc_start: 0.7657 (tp) cc_final: 0.7002 (pp)
  outliers start: 52
  outliers final: 44
  residues processed: 134
  average time/residue: 0.0673
  time to fit residues: 13.0063
Evaluate side-chains
  140 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 88
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2822 LEU
Chi-restraints excluded: chain A residue 2850 ILE
Chi-restraints excluded: chain A residue 2891 HIS
Chi-restraints excluded: chain A residue 2928 SER
Chi-restraints excluded: chain A residue 2933 CYS
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2944 SER
Chi-restraints excluded: chain A residue 2963 ILE
Chi-restraints excluded: chain A residue 2974 LEU
Chi-restraints excluded: chain A residue 2975 VAL
Chi-restraints excluded: chain A residue 3077 PHE
Chi-restraints excluded: chain A residue 3106 ASN
Chi-restraints excluded: chain A residue 3114 HIS
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 3384 THR
Chi-restraints excluded: chain A residue 3385 THR
Chi-restraints excluded: chain A residue 3399 LEU
Chi-restraints excluded: chain A residue 3402 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  360 GLN
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  381 PHE
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  427 ILE
Chi-restraints excluded: chain B residue  464 GLU
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   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 N residue    5 GLN
Chi-restraints excluded: chain N residue   18 LEU
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   22 CYS
Chi-restraints excluded: chain N residue   32 VAL
Chi-restraints excluded: chain N residue   38 ARG
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   84 ASN
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain R residue   79 VAL
Chi-restraints excluded: chain R residue   94 ASP
Chi-restraints excluded: chain R residue  135 LEU
Chi-restraints excluded: chain R residue  136 ASP
Chi-restraints excluded: chain R residue  155 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.1980
   chunk 98 optimal weight:    0.0370
   chunk 46 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0870
   chunk 52 optimal weight:    0.3980
   chunk 84 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0970
   overall best weight:    0.1234

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

Flipped N/Q/H residues before XYZ refinement:
A3114 HIS
** 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 = 0.4110 r_free = 0.4110 target = 0.115062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101763 restraints weight = 23193.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.103353 restraints weight = 14096.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.104368 restraints weight = 9973.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.104992 restraints weight = 7911.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.105467 restraints weight = 6822.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2294

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= 0.116
  Angle     :  0.680  13.369  10438  Z= 0.334
  Chirality :  0.043   0.218   1204
  Planarity :  0.004   0.048   1357
  Dihedral  :  5.541  55.118   1145
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 32.50 %
    Favored  : 63.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.27), residues: 1006
  helix:  0.91 (0.51), residues: 122
  sheet: -1.71 (0.25), residues: 431
  loop : -1.38 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A3389 
 TYR   0.021   0.001   TYR A3177 
 PHE   0.020   0.001   PHE B 340 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.011   0.001   HIS A3114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7638)
  covalent geometry    : angle       0.66065 (10408)
  SS BOND              : bond        0.00190 (   12)
  SS BOND              : angle       0.66065 (   24)
  hydrogen bonds       : bond        0.02770 (  278)
  hydrogen bonds       : angle       5.69767 (  759)
  link_NAG-ASN         : bond        0.01536 (    2)
  link_NAG-ASN         : angle       6.74215 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1424.50 seconds
wall clock time: 25 minutes 20.88 seconds (1520.88 seconds total)