Starting phenix.real_space_refine
on Tue Mar  3 16:11:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2026/7x7t_33047.cif"
  }
  resolution = 3.48
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4323      2.51       5
     N    1123      2.21       5
     O    1344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6815
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "G"
      Number of atoms: 1494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1494
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 9, 'TRANS': 177}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 853
          Classifications: {'peptide': 111}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 946
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
    Chain: "B"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 827
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103}
    Chain: "A"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 929
          Classifications: {'peptide': 119}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "D"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 831
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 921
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.54, per 1000 atoms: 0.23
  Number of scatterers: 6815
  At special positions: 0
  Unit cell: (84.802, 94.138, 112.81, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1344      8.00
     N    1123      7.00
     C    4323      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=1.57
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.02

  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 G 601 " - " ASN G 343 "
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 245.8 milliseconds
  

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1580

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 24 sheets defined
      5.4% alpha, 26.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'G' and resid 365 through 370
      removed outlier: 3.649A  pdb=" N   ASN G 370 " --> pdb=" O   SER G 366 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 386 through 390
      removed outlier: 4.116A  pdb=" N   LEU G 390 " --> pdb=" O   LEU G 387 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 407
      No H-bonds generated for 'chain 'G' and resid 405 through 407'
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.719A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 65
      removed outlier: 3.715A  pdb=" N   GLU H  65 " --> pdb=" O   LEU H  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 65'
    Processing helix  chain 'H' and resid 74 through 77
      removed outlier: 3.617A  pdb=" N   ASN H  77 " --> pdb=" O   LYS H  74 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 74 through 77'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.747A  pdb=" N   ILE B  83 " --> pdb=" O   GLN B  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.663A  pdb=" N   SER A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.591A  pdb=" N   TYR C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 356 through 358
      removed outlier: 3.509A  pdb=" N   ILE G 402 " --> pdb=" O   TYR G 508 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU G 513 " --> pdb=" O   CYS G 432 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR G 376 " --> pdb=" O   ALA G 435 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 473 through 474
      removed outlier: 3.616A  pdb=" N   TYR G 473 " --> pdb=" O   TYR G 489 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR G 489 " --> pdb=" O   TYR G 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.649A  pdb=" N   SER L   7 " --> pdb=" O   SER L  22 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   SER L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE L  79 " --> pdb=" O   ALA L  19 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 11 through 14
      removed outlier: 3.997A  pdb=" N   THR L 106 " --> pdb=" O   TYR L  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41
      removed outlier: 6.839A  pdb=" N   TRP L  39 " --> pdb=" O   LEU L  51 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.580A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLN H   5 " --> pdb=" O   LYS H  23 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS H  23 " --> pdb=" O   GLN H   5 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.679A  pdb=" N   THR H 115 " --> pdb=" O   PHE H  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 18 through 19
    Processing sheet with id=AA9, first strand: chain 'H' and resid 49 through 52
      removed outlier: 3.769A  pdb=" N   GLY H  57 " --> pdb=" O   ASP H  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 72 through 73
      removed outlier: 3.800A  pdb=" N   ASP H  73 " --> pdb=" O   THR H  78 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 19 through 24
      removed outlier: 3.845A  pdb=" N   ASP B  70 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER B  67 " --> pdb=" O   ASP B  70 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 54 through 55
      removed outlier: 6.783A  pdb=" N   LEU B  54 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLN B  90 " --> pdb=" O   THR B  97 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B  97 " --> pdb=" O   GLN B  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 85 through 86
      removed outlier: 3.673A  pdb=" N   TYR B  86 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.578A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 12
      removed outlier: 3.586A  pdb=" N   GLN A  39 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   LYS A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   TRP A  47 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 6
      removed outlier: 3.833A  pdb=" N   VAL D  19 " --> pdb=" O   ILE D  75 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASN D  70 " --> pdb=" O   SER D  67 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER D  67 " --> pdb=" O   ASN D  70 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 11
    Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46
    Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 11
    Processing sheet with id=AC4, first strand: chain 'C' and resid 18 through 20
    Processing sheet with id=AC5, first strand: chain 'C' and resid 49 through 51
    Processing sheet with id=AC6, first strand: chain 'C' and resid 97 through 98

    162 hydrogen bonds defined for protein.
    363 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: 0.92

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1107
        1.29 -     1.42: 2023
        1.42 -     1.55: 3825
        1.55 -     1.68: 3
        1.68 -     1.81: 30
  Bond restraints: 6988
  Sorted by residual:
  bond pdb=" C   ASN G 334 "
       pdb=" O   ASN G 334 "
    ideal  model  delta    sigma   weight residual
    1.235  1.160  0.075 1.21e-02 6.83e+03 3.86e+01
  bond pdb=" C   GLN C   3 "
       pdb=" O   GLN C   3 "
    ideal  model  delta    sigma   weight residual
    1.236  1.302 -0.066 1.19e-02 7.06e+03 3.07e+01
  bond pdb=" C   LYS C  23 "
       pdb=" O   LYS C  23 "
    ideal  model  delta    sigma   weight residual
    1.235  1.299 -0.063 1.23e-02 6.61e+03 2.64e+01
  bond pdb=" C   LEU C   4 "
       pdb=" O   LEU C   4 "
    ideal  model  delta    sigma   weight residual
    1.236  1.289 -0.053 1.14e-02 7.69e+03 2.15e+01
  bond pdb=" CA  TRP C  47 "
       pdb=" C   TRP C  47 "
    ideal  model  delta    sigma   weight residual
    1.527  1.470  0.057 1.35e-02 5.49e+03 1.77e+01
  ... (remaining 6983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.86: 9240
        2.86 -     5.71: 220
        5.71 -     8.57: 26
        8.57 -    11.42: 6
       11.42 -    14.28: 4
  Bond angle restraints: 9496
  Sorted by residual:
  angle pdb=" N   PHE G 338 "
        pdb=" CA  PHE G 338 "
        pdb=" C   PHE G 338 "
      ideal   model   delta    sigma   weight residual
     112.92   98.64   14.28 1.23e+00 6.61e-01 1.35e+02
  angle pdb=" N   ILE D  29 "
        pdb=" CA  ILE D  29 "
        pdb=" C   ILE D  29 "
      ideal   model   delta    sigma   weight residual
     108.11   93.91   14.20 1.40e+00 5.10e-01 1.03e+02
  angle pdb=" N   ASN L  35 "
        pdb=" CA  ASN L  35 "
        pdb=" C   ASN L  35 "
      ideal   model   delta    sigma   weight residual
     110.17   96.65   13.52 1.61e+00 3.86e-01 7.05e+01
  angle pdb=" N   TRP C  47 "
        pdb=" CA  TRP C  47 "
        pdb=" C   TRP C  47 "
      ideal   model   delta    sigma   weight residual
     110.53  120.04   -9.51 1.32e+00 5.74e-01 5.19e+01
  angle pdb=" CA  TYR L  91 "
        pdb=" C   TYR L  91 "
        pdb=" O   TYR L  91 "
      ideal   model   delta    sigma   weight residual
     122.01  115.31    6.70 1.05e+00 9.07e-01 4.07e+01
  ... (remaining 9491 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 3682
       17.03 -    34.06: 320
       34.06 -    51.09: 48
       51.09 -    68.12: 15
       68.12 -    85.15: 7
  Dihedral angle restraints: 4072
    sinusoidal: 1566
      harmonic: 2506
  Sorted by residual:
  dihedral pdb=" C   CYS G 336 "
           pdb=" N   CYS G 336 "
           pdb=" CA  CYS G 336 "
           pdb=" CB  CYS G 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.63  -13.97     0      2.50e+00 1.60e-01 3.12e+01
  dihedral pdb=" C   THR A 113 "
           pdb=" N   THR A 113 "
           pdb=" CA  THR A 113 "
           pdb=" CB  THR A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -109.65  -12.35     0      2.50e+00 1.60e-01 2.44e+01
  dihedral pdb=" CA  ASN D  31 "
           pdb=" C   ASN D  31 "
           pdb=" N   TRP D  32 "
           pdb=" CA  TRP D  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.69  -24.31     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 4069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 898
       0.090 -    0.181: 100
       0.181 -    0.271: 14
       0.271 -    0.361: 4
       0.361 -    0.451: 2
  Chirality restraints: 1018
  Sorted by residual:
  chirality pdb=" CA  TYR D  91 "
            pdb=" N   TYR D  91 "
            pdb=" C   TYR D  91 "
            pdb=" CB  TYR D  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.09e+00
  chirality pdb=" CA  TYR L  36 "
            pdb=" N   TYR L  36 "
            pdb=" C   TYR L  36 "
            pdb=" CB  TYR L  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  CYS G 336 "
            pdb=" N   CYS G 336 "
            pdb=" C   CYS G 336 "
            pdb=" CB  CYS G 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 1015 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS G 336 "   -0.013 2.00e-02 2.50e+03   2.62e-02 6.88e+00
        pdb=" C   CYS G 336 "    0.045 2.00e-02 2.50e+03
        pdb=" O   CYS G 336 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO G 337 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G 335 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.40e+00
        pdb=" C   LEU G 335 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   LEU G 335 "    0.016 2.00e-02 2.50e+03
        pdb=" N   CYS G 336 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  77 "   -0.013 2.00e-02 2.50e+03   2.52e-02 6.34e+00
        pdb=" C   ASN B  77 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASN B  77 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B  78 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 418
        2.72 -     3.26: 6442
        3.26 -     3.81: 10227
        3.81 -     4.35: 13116
        4.35 -     4.90: 23035
  Nonbonded interactions: 53238
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  24 "
            pdb=" OG  SER A  77 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OD2 ASP C  73 "
            pdb=" OG  SER C  75 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" NE2 GLN B  38 "
            pdb=" OE1 GLN A  39 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   SER D  60 "
            pdb=" OG  SER D  60 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OH  TYR C  60 "
            pdb=" N   LEU C  70 "
     model   vdw
     2.332 3.120
  ... (remaining 53233 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=0.67 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5886
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      :  0.009   0.463   6997  Z= 0.516
  Angle     :  1.052  14.279   9515  Z= 0.648
  Chirality :  0.063   0.451   1018
  Planarity :  0.006   0.058   1217
  Dihedral  : 13.408  85.150   2468
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.96 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.95 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -4.53 (0.24), residues: 855
  helix: -5.31 (0.19), residues: 27
  sheet: -2.86 (0.26), residues: 317
  loop : -3.06 (0.23), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 466 
 TYR   0.025   0.002   TYR D  91 
 PHE   0.027   0.002   PHE A  29 
 TRP   0.020   0.003   TRP C  47 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00676 ( 6988)
  covalent geometry    : angle       1.03790 ( 9496)
  SS BOND              : bond        0.16360 (    8)
  SS BOND              : angle       3.77047 (   16)
  hydrogen bonds       : bond        0.29655 (  155)
  hydrogen bonds       : angle      11.08529 (  363)
  link_NAG-ASN         : bond        0.00217 (    1)
  link_NAG-ASN         : angle       4.76387 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: G  424 LYS cc_start: 0.5455 (tttp) cc_final: 0.5194 (ttmt)
REVERT: G  519 HIS cc_start: 0.6628 (m-70) cc_final: 0.4918 (t-170)
REVERT: L   49 LYS cc_start: 0.6549 (mttt) cc_final: 0.5833 (ptmm)
REVERT: H   19 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7252 (mtpp)
REVERT: H  109 ASP cc_start: 0.7730 (m-30) cc_final: 0.7495 (m-30)
REVERT: B   17 ASP cc_start: 0.7873 (m-30) cc_final: 0.7462 (m-30)
REVERT: A   59 ARG cc_start: 0.5869 (mtt-85) cc_final: 0.5258 (mtm180)
REVERT: D   13 VAL cc_start: 0.6820 (m) cc_final: 0.6524 (p)
REVERT: D   78 LEU cc_start: 0.6694 (mp) cc_final: 0.6390 (mp)
REVERT: D  105 GLU cc_start: 0.3939 (tp30) cc_final: 0.2873 (tp30)
REVERT: C   32 TYR cc_start: 0.7295 (m-80) cc_final: 0.7084 (m-80)
REVERT: C   60 TYR cc_start: 0.8110 (m-80) cc_final: 0.7439 (m-80)
REVERT: C   74 LYS cc_start: 0.7517 (mtpt) cc_final: 0.6523 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0754
  time to fit residues: 19.8600
Evaluate side-chains
  156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
G 422 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  34 ASN
D  38 GLN
C   6 GLN
C  39 GLN
** C  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.184113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.157832 restraints weight = 7634.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 2.32
r_work: 0.3641 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3070
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3070 r_free = 0.3070    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3070
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6997  Z= 0.135
  Angle     :  0.630  10.981   9515  Z= 0.322
  Chirality :  0.044   0.172   1018
  Planarity :  0.005   0.045   1217
  Dihedral  :  5.888  44.815    980
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.67 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -3.77 (0.25), residues: 855
  helix: -5.18 (0.26), residues: 26
  sheet: -2.45 (0.26), residues: 330
  loop : -2.40 (0.24), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  61 
 TYR   0.019   0.001   TYR D  91 
 PHE   0.017   0.002   PHE G 490 
 TRP   0.013   0.001   TRP C  47 
 HIS   0.002   0.001   HIS H  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6988)
  covalent geometry    : angle       0.62707 ( 9496)
  SS BOND              : bond        0.00329 (    8)
  SS BOND              : angle       0.77224 (   16)
  hydrogen bonds       : bond        0.03911 (  155)
  hydrogen bonds       : angle       7.51671 (  363)
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       3.43909 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 155
  time to evaluate  : 0.237 
Fit side-chains
REVERT: G  384 PRO cc_start: 0.8484 (Cg_endo) cc_final: 0.8284 (Cg_exo)
REVERT: G  405 ASP cc_start: 0.8800 (t0) cc_final: 0.8568 (t0)
REVERT: G  519 HIS cc_start: 0.8463 (m-70) cc_final: 0.7122 (t-170)
REVERT: H   19 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7760 (mtpt)
REVERT: H   51 PHE cc_start: 0.8239 (t80) cc_final: 0.7675 (t80)
REVERT: B   61 ARG cc_start: 0.8289 (mtm110) cc_final: 0.8078 (mtm-85)
REVERT: D   78 LEU cc_start: 0.8301 (mp) cc_final: 0.8064 (mp)
REVERT: D  105 GLU cc_start: 0.5256 (tp30) cc_final: 0.3320 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 158
  average time/residue: 0.0758
  time to fit residues: 16.2895
Evaluate side-chains
  150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 82 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
G 370 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  77 ASN
D  42 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.179019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.152803 restraints weight = 7636.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.32
r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   6997  Z= 0.213
  Angle     :  0.666  13.234   9515  Z= 0.338
  Chirality :  0.044   0.142   1018
  Planarity :  0.005   0.039   1217
  Dihedral  :  5.875  39.107    980
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.40 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -3.47 (0.26), residues: 855
  helix: -5.09 (0.28), residues: 27
  sheet: -2.31 (0.25), residues: 350
  loop : -2.09 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  63 
 TYR   0.019   0.002   TYR D  91 
 PHE   0.023   0.002   PHE G 377 
 TRP   0.013   0.002   TRP C  47 
 HIS   0.007   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 6988)
  covalent geometry    : angle       0.66181 ( 9496)
  SS BOND              : bond        0.00414 (    8)
  SS BOND              : angle       1.09425 (   16)
  hydrogen bonds       : bond        0.03641 (  155)
  hydrogen bonds       : angle       6.92970 (  363)
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       3.93780 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.151 
Fit side-chains
REVERT: G  399 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8381 (p)
REVERT: G  405 ASP cc_start: 0.8668 (t0) cc_final: 0.8455 (t0)
REVERT: H   19 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8032 (mtpt)
REVERT: B    4 MET cc_start: 0.8584 (tpp) cc_final: 0.8375 (mmm)
REVERT: D   39 LYS cc_start: 0.8453 (pttp) cc_final: 0.8090 (mtmm)
REVERT: D  105 GLU cc_start: 0.5273 (tp30) cc_final: 0.3266 (tp30)
  outliers start: 18
  outliers final: 15
  residues processed: 152
  average time/residue: 0.0780
  time to fit residues: 16.0152
Evaluate side-chains
  153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  445 VAL
Chi-restraints excluded: chain G residue  460 ASN
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.182184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155731 restraints weight = 7851.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.33
r_work: 0.3640 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   6997  Z= 0.199
  Angle     :  0.650  12.833   9515  Z= 0.328
  Chirality :  0.044   0.204   1018
  Planarity :  0.005   0.039   1217
  Dihedral  :  5.670  31.001    980
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 16.49 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -3.17 (0.26), residues: 855
  helix: -5.13 (0.30), residues: 26
  sheet: -2.08 (0.26), residues: 349
  loop : -1.90 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  63 
 TYR   0.020   0.002   TYR C  32 
 PHE   0.019   0.002   PHE A  29 
 TRP   0.012   0.002   TRP G 436 
 HIS   0.007   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 6988)
  covalent geometry    : angle       0.64563 ( 9496)
  SS BOND              : bond        0.00399 (    8)
  SS BOND              : angle       1.04139 (   16)
  hydrogen bonds       : bond        0.03229 (  155)
  hydrogen bonds       : angle       6.50454 (  363)
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       3.98566 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.215 
Fit side-chains
REVERT: G  399 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8379 (p)
REVERT: G  405 ASP cc_start: 0.8779 (t0) cc_final: 0.8504 (t0)
REVERT: L  111 LYS cc_start: 0.6436 (mtpp) cc_final: 0.6096 (mmmt)
REVERT: H   19 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8132 (mtpt)
REVERT: B   90 GLN cc_start: 0.8982 (pp30) cc_final: 0.8702 (pp30)
REVERT: A  103 ASN cc_start: 0.8854 (m-40) cc_final: 0.8565 (m-40)
REVERT: D   39 LYS cc_start: 0.8549 (pttp) cc_final: 0.8290 (mtmm)
REVERT: D  105 GLU cc_start: 0.5313 (tp30) cc_final: 0.3319 (tp30)
REVERT: C   60 TYR cc_start: 0.9102 (m-80) cc_final: 0.8843 (m-80)
  outliers start: 26
  outliers final: 20
  residues processed: 153
  average time/residue: 0.0750
  time to fit residues: 15.6753
Evaluate side-chains
  157 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  398 ASP
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  445 VAL
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  460 ASN
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain D residue   56 THR
Chi-restraints excluded: chain C residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 63 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 GLN
A 111 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.170871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145875 restraints weight = 7895.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.89
r_work: 0.3177 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3026
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3026 r_free = 0.3026    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3026
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087   6997  Z= 0.262
  Angle     :  0.699  14.172   9515  Z= 0.355
  Chirality :  0.045   0.197   1018
  Planarity :  0.005   0.040   1217
  Dihedral  :  5.748  32.657    980
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 16.76 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -3.11 (0.27), residues: 855
  helix: -5.15 (0.29), residues: 26
  sheet: -2.05 (0.26), residues: 355
  loop : -1.83 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  63 
 TYR   0.018   0.002   TYR D  91 
 PHE   0.022   0.002   PHE G 400 
 TRP   0.013   0.002   TRP L  96 
 HIS   0.007   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 ( 6988)
  covalent geometry    : angle       0.69383 ( 9496)
  SS BOND              : bond        0.00413 (    8)
  SS BOND              : angle       1.15925 (   16)
  hydrogen bonds       : bond        0.03376 (  155)
  hydrogen bonds       : angle       6.41703 (  363)
  link_NAG-ASN         : bond        0.00025 (    1)
  link_NAG-ASN         : angle       4.50132 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.250 
Fit side-chains
REVERT: G  399 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8355 (p)
REVERT: G  405 ASP cc_start: 0.8672 (t0) cc_final: 0.8429 (t0)
REVERT: G  418 ILE cc_start: 0.9121 (mm) cc_final: 0.8919 (mm)
REVERT: G  501 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7792 (m110)
REVERT: G  516 GLU cc_start: 0.4969 (tp30) cc_final: 0.4760 (tp30)
REVERT: L  111 LYS cc_start: 0.6492 (mtpp) cc_final: 0.6095 (mmmt)
REVERT: H   19 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8005 (mtpp)
REVERT: A  103 ASN cc_start: 0.8793 (m-40) cc_final: 0.8467 (m-40)
REVERT: D   39 LYS cc_start: 0.8440 (pttp) cc_final: 0.8117 (mtmm)
  outliers start: 35
  outliers final: 27
  residues processed: 159
  average time/residue: 0.0705
  time to fit residues: 15.6320
Evaluate side-chains
  166 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  398 ASP
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  438 SER
Chi-restraints excluded: chain G residue  445 VAL
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  460 ASN
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain G residue  501 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   15 LEU
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   19 VAL
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain D residue   56 THR
Chi-restraints excluded: chain C residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 47 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.179106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156438 restraints weight = 7732.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.99
r_work: 0.3632 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3466 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6997  Z= 0.165
  Angle     :  0.623  12.219   9515  Z= 0.313
  Chirality :  0.042   0.188   1018
  Planarity :  0.004   0.042   1217
  Dihedral  :  5.412  30.639    980
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.66 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -2.81 (0.27), residues: 855
  helix: -5.09 (0.32), residues: 26
  sheet: -1.80 (0.26), residues: 364
  loop : -1.65 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 408 
 TYR   0.022   0.002   TYR C  32 
 PHE   0.018   0.002   PHE A  29 
 TRP   0.012   0.002   TRP G 436 
 HIS   0.006   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6988)
  covalent geometry    : angle       0.61908 ( 9496)
  SS BOND              : bond        0.00291 (    8)
  SS BOND              : angle       0.75790 (   16)
  hydrogen bonds       : bond        0.02964 (  155)
  hydrogen bonds       : angle       6.00971 (  363)
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       4.08580 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: G  399 SER cc_start: 0.8660 (OUTLIER) cc_final: 0.8340 (p)
REVERT: G  405 ASP cc_start: 0.8678 (t0) cc_final: 0.8425 (t0)
REVERT: G  516 GLU cc_start: 0.5019 (tp30) cc_final: 0.4734 (tp30)
REVERT: L  111 LYS cc_start: 0.6553 (mtpp) cc_final: 0.6209 (mmmt)
REVERT: H   19 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8088 (mtpp)
REVERT: B    4 MET cc_start: 0.8336 (tpp) cc_final: 0.8104 (mmm)
REVERT: B   90 GLN cc_start: 0.8926 (pp30) cc_final: 0.8661 (pp30)
REVERT: A  103 ASN cc_start: 0.8838 (m-40) cc_final: 0.8543 (m-40)
REVERT: D   79 GLN cc_start: 0.8201 (mt0) cc_final: 0.7847 (mp10)
  outliers start: 25
  outliers final: 20
  residues processed: 150
  average time/residue: 0.0792
  time to fit residues: 16.1100
Evaluate side-chains
  152 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  350 VAL
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  398 ASP
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  445 VAL
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue   95 SER
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain C residue   52 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0670
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   overall best weight:    0.3574

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.183954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.158373 restraints weight = 7563.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 2.25
r_work: 0.3643 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3311
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.66   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3311 r_free = 0.3311    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3311
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6997  Z= 0.105
  Angle     :  0.569  10.229   9515  Z= 0.283
  Chirality :  0.041   0.201   1018
  Planarity :  0.004   0.041   1217
  Dihedral  :  4.956  25.903    980
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 19.07 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -2.42 (0.28), residues: 855
  helix: -4.87 (0.43), residues: 20
  sheet: -1.56 (0.27), residues: 358
  loop : -1.43 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 408 
 TYR   0.019   0.001   TYR C  32 
 PHE   0.027   0.001   PHE G 456 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.006   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6988)
  covalent geometry    : angle       0.56603 ( 9496)
  SS BOND              : bond        0.00247 (    8)
  SS BOND              : angle       0.51828 (   16)
  hydrogen bonds       : bond        0.02592 (  155)
  hydrogen bonds       : angle       5.50993 (  363)
  link_NAG-ASN         : bond        0.00075 (    1)
  link_NAG-ASN         : angle       3.60351 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: G  405 ASP cc_start: 0.8680 (t0) cc_final: 0.8367 (t0)
REVERT: G  516 GLU cc_start: 0.5051 (tp30) cc_final: 0.4814 (tp30)
REVERT: L  111 LYS cc_start: 0.6572 (mtpp) cc_final: 0.6251 (mmmt)
REVERT: H   19 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8135 (mtpp)
REVERT: B    4 MET cc_start: 0.8335 (tpp) cc_final: 0.8058 (mmm)
REVERT: D   79 GLN cc_start: 0.8219 (mt0) cc_final: 0.7909 (mp10)
REVERT: D   92 TRP cc_start: 0.8462 (t-100) cc_final: 0.8017 (t-100)
  outliers start: 24
  outliers final: 18
  residues processed: 145
  average time/residue: 0.0698
  time to fit residues: 14.0592
Evaluate side-chains
  142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain C residue    2 ILE
Chi-restraints excluded: chain C residue   34 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.180371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.155543 restraints weight = 7701.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.26
r_work: 0.3656 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3332
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3332 r_free = 0.3332    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3332
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6997  Z= 0.173
  Angle     :  0.613  10.526   9515  Z= 0.307
  Chirality :  0.043   0.212   1018
  Planarity :  0.005   0.093   1217
  Dihedral  :  5.126  26.024    980
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.21 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -2.41 (0.28), residues: 855
  helix: -5.02 (0.32), residues: 26
  sheet: -1.58 (0.26), residues: 364
  loop : -1.30 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 408 
 TYR   0.018   0.002   TYR C  32 
 PHE   0.031   0.002   PHE G 456 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.010   0.002   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6988)
  covalent geometry    : angle       0.60885 ( 9496)
  SS BOND              : bond        0.00289 (    8)
  SS BOND              : angle       0.72405 (   16)
  hydrogen bonds       : bond        0.02824 (  155)
  hydrogen bonds       : angle       5.66010 (  363)
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       3.82626 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: G  399 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8256 (p)
REVERT: G  405 ASP cc_start: 0.8710 (t0) cc_final: 0.8417 (t0)
REVERT: G  420 ASP cc_start: 0.8458 (m-30) cc_final: 0.8166 (m-30)
REVERT: G  501 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (m110)
REVERT: G  516 GLU cc_start: 0.5205 (tp30) cc_final: 0.4941 (tp30)
REVERT: L  111 LYS cc_start: 0.6538 (mtpp) cc_final: 0.6171 (mmmt)
REVERT: H   19 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8137 (mtpp)
REVERT: B    4 MET cc_start: 0.8414 (tpp) cc_final: 0.8132 (mmm)
REVERT: A   43 GLN cc_start: 0.8488 (mp10) cc_final: 0.8257 (mp10)
REVERT: D   79 GLN cc_start: 0.8187 (mt0) cc_final: 0.7862 (mp10)
REVERT: C   60 TYR cc_start: 0.9108 (m-80) cc_final: 0.8811 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 141
  average time/residue: 0.0746
  time to fit residues: 14.5826
Evaluate side-chains
  147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  460 ASN
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain G residue  501 ASN
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain C residue    2 ILE
Chi-restraints excluded: chain C residue   52 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0670
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0470
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.5416

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.183045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.157207 restraints weight = 7696.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.27
r_work: 0.3682 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6997  Z= 0.124
  Angle     :  0.580   9.553   9515  Z= 0.289
  Chirality :  0.041   0.205   1018
  Planarity :  0.005   0.087   1217
  Dihedral  :  4.929  24.949    980
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.89 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -2.17 (0.28), residues: 855
  helix: -4.57 (0.59), residues: 14
  sheet: -1.43 (0.26), residues: 370
  loop : -1.26 (0.28), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 408 
 TYR   0.018   0.001   TYR C  32 
 PHE   0.031   0.001   PHE G 456 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.010   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6988)
  covalent geometry    : angle       0.57681 ( 9496)
  SS BOND              : bond        0.00222 (    8)
  SS BOND              : angle       0.55347 (   16)
  hydrogen bonds       : bond        0.02631 (  155)
  hydrogen bonds       : angle       5.40749 (  363)
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       3.58254 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: G  399 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8270 (p)
REVERT: G  405 ASP cc_start: 0.8668 (t0) cc_final: 0.8371 (t0)
REVERT: G  516 GLU cc_start: 0.5172 (tp30) cc_final: 0.4896 (tp30)
REVERT: G  519 HIS cc_start: 0.8394 (m-70) cc_final: 0.6808 (t-170)
REVERT: L  111 LYS cc_start: 0.6534 (mtpp) cc_final: 0.6192 (mmmt)
REVERT: H   19 LYS cc_start: 0.8553 (mtpt) cc_final: 0.8237 (mtpt)
REVERT: B    4 MET cc_start: 0.8389 (tpp) cc_final: 0.8085 (mmm)
REVERT: D    9 SER cc_start: 0.8389 (m) cc_final: 0.7668 (t)
REVERT: D   79 GLN cc_start: 0.8217 (mt0) cc_final: 0.7892 (mp10)
REVERT: D   92 TRP cc_start: 0.8508 (t-100) cc_final: 0.8009 (t-100)
  outliers start: 23
  outliers final: 18
  residues processed: 144
  average time/residue: 0.0751
  time to fit residues: 14.8246
Evaluate side-chains
  146 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  398 ASP
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  445 VAL
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain C residue   52 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0670
   chunk 54 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.183321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157699 restraints weight = 7626.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.43
r_work: 0.3643 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3472 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3073 r_free = 0.3073    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6997  Z= 0.124
  Angle     :  0.578   9.574   9515  Z= 0.288
  Chirality :  0.041   0.212   1018
  Planarity :  0.005   0.080   1217
  Dihedral  :  4.878  24.700    980
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.03 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -2.04 (0.28), residues: 855
  helix: -4.40 (0.65), residues: 14
  sheet: -1.34 (0.27), residues: 371
  loop : -1.19 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 408 
 TYR   0.019   0.001   TYR C  32 
 PHE   0.014   0.001   PHE A  29 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.010   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6988)
  covalent geometry    : angle       0.57464 ( 9496)
  SS BOND              : bond        0.00219 (    8)
  SS BOND              : angle       0.55014 (   16)
  hydrogen bonds       : bond        0.02578 (  155)
  hydrogen bonds       : angle       5.35713 (  363)
  link_NAG-ASN         : bond        0.00098 (    1)
  link_NAG-ASN         : angle       3.56261 (    3)

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

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

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1710 Ramachandran restraints generated.
    855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: G  399 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8235 (p)
REVERT: G  405 ASP cc_start: 0.8668 (t0) cc_final: 0.8376 (t0)
REVERT: G  420 ASP cc_start: 0.8372 (m-30) cc_final: 0.8060 (m-30)
REVERT: G  516 GLU cc_start: 0.5185 (tp30) cc_final: 0.4914 (tp30)
REVERT: G  519 HIS cc_start: 0.8350 (m-70) cc_final: 0.6809 (t-170)
REVERT: L  111 LYS cc_start: 0.6476 (mtpp) cc_final: 0.6157 (mmmt)
REVERT: H   19 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8009 (mtpt)
REVERT: B    4 MET cc_start: 0.8372 (tpp) cc_final: 0.8055 (mmm)
REVERT: D    9 SER cc_start: 0.8443 (m) cc_final: 0.7729 (t)
REVERT: D   79 GLN cc_start: 0.8166 (mt0) cc_final: 0.7889 (mp10)
REVERT: D   92 TRP cc_start: 0.8517 (t-100) cc_final: 0.8009 (t-100)
  outliers start: 22
  outliers final: 19
  residues processed: 147
  average time/residue: 0.0727
  time to fit residues: 14.8178
Evaluate side-chains
  153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  358 ILE
Chi-restraints excluded: chain G residue  385 THR
Chi-restraints excluded: chain G residue  398 ASP
Chi-restraints excluded: chain G residue  399 SER
Chi-restraints excluded: chain G residue  452 LEU
Chi-restraints excluded: chain G residue  460 ASN
Chi-restraints excluded: chain G residue  489 TYR
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   37 VAL
Chi-restraints excluded: chain L residue   73 THR
Chi-restraints excluded: chain L residue  106 THR
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   51 THR
Chi-restraints excluded: chain A residue    6 GLN
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain D residue   30 ASN
Chi-restraints excluded: chain C residue   52 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0470
   chunk 9 optimal weight:    0.2980
   chunk 45 optimal weight:    0.4980
   chunk 73 optimal weight:    0.0370
   chunk 22 optimal weight:    0.2980
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.2356

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

Flipped N/Q/H residues before XYZ refinement:
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 GLN
D  42 ASN
C   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.186874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.162054 restraints weight = 7594.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 2.18
r_work: 0.3675 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3389
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3389 r_free = 0.3389    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3389
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6997  Z= 0.094
  Angle     :  0.558   9.819   9515  Z= 0.278
  Chirality :  0.041   0.153   1018
  Planarity :  0.004   0.075   1217
  Dihedral  :  4.666  23.859    980
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.71 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 are not related in a simple way.
  whole: -1.87 (0.28), residues: 855
  helix: -4.31 (0.67), residues: 14
  sheet: -1.13 (0.27), residues: 366
  loop : -1.17 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 408 
 TYR   0.018   0.001   TYR C  32 
 PHE   0.015   0.001   PHE B  87 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.010   0.001   HIS C  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6988)
  covalent geometry    : angle       0.55512 ( 9496)
  SS BOND              : bond        0.00196 (    8)
  SS BOND              : angle       0.41660 (   16)
  hydrogen bonds       : bond        0.02441 (  155)
  hydrogen bonds       : angle       5.10729 (  363)
  link_NAG-ASN         : bond        0.00112 (    1)
  link_NAG-ASN         : angle       3.23154 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1927.69 seconds
wall clock time: 33 minutes 41.67 seconds (2021.67 seconds total)