Starting phenix.real_space_refine
on Wed Mar  4 03:57:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a5r_11648/03_2026/7a5r_11648.cif"
  }
  resolution = 3.7
  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=   0.002 sd=   0.038
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      40      5.16       5
     C    6760      2.51       5
     N    1748      2.21       5
     O    2060      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 114 residue(s): 0.01s

  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: 10608
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1595
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1568
          Classifications: {'peptide': 202}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 190}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2113
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 17, 'TRANS': 246}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    I, M, B, D
  Time building chain proxies: 2.54, per 1000 atoms: 0.24
  Number of scatterers: 10608
  At special positions: 0
  Unit cell: (138.049, 166.311, 71.742, 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      40     16.00
     O    2060      8.00
     N    1748      7.00
     C    6760      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 144 " - pdb=" SG  CYS I 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 140 " - pdb=" SG  CYS M 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 343 "
      " NAG D   1 " - " ASN B 343 "
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 448.8 milliseconds
  

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 30 sheets defined
      6.8% alpha, 33.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'H' and resid 160 through 162
      No H-bonds generated for 'chain 'H' and resid 160 through 162'
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.689A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS L 132 " --> pdb=" O   ASP L 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER L 133 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY L 134 " --> pdb=" O   GLN L 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 127 through 134'
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.964A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR A 369 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 365 through 369'
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.237A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.759A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.964A  pdb=" N   LEU B 368 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   TYR B 369 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 365 through 369'
    Processing helix  chain 'B' and resid 383 through 388
      removed outlier: 4.238A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 3.758A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.783A  pdb=" N   ASP B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 127 through 134
      removed outlier: 3.690A  pdb=" N   LEU M 131 " --> pdb=" O   SER M 127 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LYS M 132 " --> pdb=" O   ASP M 128 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER M 133 " --> pdb=" O   GLU M 129 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY M 134 " --> pdb=" O   GLN M 130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 127 through 134'
    Processing helix  chain 'I' and resid 160 through 162
      No H-bonds generated for 'chain 'I' and resid 160 through 162'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR H 116 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL H 108 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.342A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS H 144 " --> pdb=" O   SER H 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER H 184 " --> pdb=" O   CYS H 144 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ASP H 148 " --> pdb=" O   TYR H 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 111 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31
      removed outlier: 3.772A  pdb=" N   LYS L  36 " --> pdb=" O   TYR L  31 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER L 120 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN L 143 " --> pdb=" O   SER L 120 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 150 through 156
      removed outlier: 3.637A  pdb=" N   TYR L 198 " --> pdb=" O   PHE L 215 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS A  49 " --> pdb=" O   LEU A 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 277 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 325 through 328
    Processing sheet with id=AB4, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.512A  pdb=" N   HIS B  49 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 277 " --> pdb=" O   HIS B  49 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 325 through 328
    Processing sheet with id=AB9, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.912A  pdb=" N   ILE B 358 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ALA B 435 " --> pdb=" O   THR B 376 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AC2, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7
    Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13
      removed outlier: 6.247A  pdb=" N   LEU M  11 " --> pdb=" O   GLU M 111 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP M  41 " --> pdb=" O   LEU M  53 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31
      removed outlier: 3.773A  pdb=" N   LYS M  36 " --> pdb=" O   TYR M  31 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124
      removed outlier: 3.879A  pdb=" N   SER M 120 " --> pdb=" O   ASN M 143 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASN M 143 " --> pdb=" O   SER M 120 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'M' and resid 150 through 156
      removed outlier: 3.637A  pdb=" N   TYR M 198 " --> pdb=" O   PHE M 215 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6
    Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY I  49 " --> pdb=" O   TRP I  36 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ARG I  38 " --> pdb=" O   TRP I  47 " (cutoff:3.500A)
      removed outlier: 5.556A  pdb=" N   TRP I  47 " --> pdb=" O   ARG I  38 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 11
      removed outlier: 3.749A  pdb=" N   GLU I  10 " --> pdb=" O   THR I 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR I 116 " --> pdb=" O   GLU I  10 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL I 108 " --> pdb=" O   GLY I  98 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 128
      removed outlier: 4.343A  pdb=" N   GLY I 143 " --> pdb=" O   LEU I 128 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS I 144 " --> pdb=" O   SER I 184 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER I 184 " --> pdb=" O   CYS I 144 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP I 148 " --> pdb=" O   TYR I 180 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR I 180 " --> pdb=" O   ASP I 148 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'I' and resid 155 through 158
      removed outlier: 4.747A  pdb=" N   TYR I 198 " --> pdb=" O   VAL I 215 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3324
        1.34 -     1.46: 2768
        1.46 -     1.58: 4730
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 10870
  Sorted by residual:
  bond pdb=" N   LEU H 174 "
       pdb=" CA  LEU H 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.24e-02 6.50e+03 5.14e+00
  bond pdb=" N   LEU I 174 "
       pdb=" CA  LEU I 174 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.027 1.24e-02 6.50e+03 4.60e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.44e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.13e+00
  ... (remaining 10865 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 14062
        1.68 -     3.36: 608
        3.36 -     5.05: 92
        5.05 -     6.73: 14
        6.73 -     8.41: 10
  Bond angle restraints: 14786
  Sorted by residual:
  angle pdb=" C   ASN B 370 "
        pdb=" CA  ASN B 370 "
        pdb=" CB  ASN B 370 "
      ideal   model   delta    sigma   weight residual
     111.91  116.08   -4.17 1.52e+00 4.33e-01 7.53e+00
  angle pdb=" CA  ILE M   2 "
        pdb=" CB  ILE M   2 "
        pdb=" CG1 ILE M   2 "
      ideal   model   delta    sigma   weight residual
     110.40  115.06   -4.66 1.70e+00 3.46e-01 7.51e+00
  angle pdb=" CA  ILE L   2 "
        pdb=" CB  ILE L   2 "
        pdb=" CG1 ILE L   2 "
      ideal   model   delta    sigma   weight residual
     110.40  115.04   -4.64 1.70e+00 3.46e-01 7.45e+00
  angle pdb=" C   ASN A 370 "
        pdb=" CA  ASN A 370 "
        pdb=" CB  ASN A 370 "
      ideal   model   delta    sigma   weight residual
     111.91  116.05   -4.14 1.52e+00 4.33e-01 7.42e+00
  angle pdb=" C   TYR M 146 "
        pdb=" N   PRO M 147 "
        pdb=" CA  PRO M 147 "
      ideal   model   delta    sigma   weight residual
     127.00  133.25   -6.25 2.40e+00 1.74e-01 6.78e+00
  ... (remaining 14781 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 5891
       17.87 -    35.75: 497
       35.75 -    53.62: 106
       53.62 -    71.49: 22
       71.49 -    89.37: 6
  Dihedral angle restraints: 6522
    sinusoidal: 2584
      harmonic: 3938
  Sorted by residual:
  dihedral pdb=" CB  CYS H 144 "
           pdb=" SG  CYS H 144 "
           pdb=" SG  CYS H 200 "
           pdb=" CB  CYS H 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.54  -36.54     1      1.00e+01 1.00e-02 1.89e+01
  dihedral pdb=" CB  CYS I 144 "
           pdb=" SG  CYS I 144 "
           pdb=" SG  CYS I 200 "
           pdb=" CB  CYS I 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  129.53  -36.53     1      1.00e+01 1.00e-02 1.89e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -122.12   36.12     1      1.00e+01 1.00e-02 1.85e+01
  ... (remaining 6519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 964
       0.035 -    0.069: 406
       0.069 -    0.104: 190
       0.104 -    0.138: 83
       0.138 -    0.173: 9
  Chirality restraints: 1652
  Sorted by residual:
  chirality pdb=" CB  ILE L  34 "
            pdb=" CA  ILE L  34 "
            pdb=" CG1 ILE L  34 "
            pdb=" CG2 ILE L  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.17 2.00e-01 2.50e+01 7.44e-01
  chirality pdb=" CB  ILE M  34 "
            pdb=" CA  ILE M  34 "
            pdb=" CG1 ILE M  34 "
            pdb=" CG2 ILE M  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.81   -0.17 2.00e-01 2.50e+01 7.08e-01
  chirality pdb=" CB  THR I  91 "
            pdb=" CA  THR I  91 "
            pdb=" OG1 THR I  91 "
            pdb=" CG2 THR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.31e-01
  ... (remaining 1649 not shown)

  Planarity restraints: 1884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 152 "    0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO H 153 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO H 153 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO H 153 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU I 152 "   -0.034 5.00e-02 4.00e+02   5.11e-02 4.18e+00
        pdb=" N   PRO I 153 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO I 153 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO I 153 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 512 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   VAL B 512 "    0.030 2.00e-02 2.50e+03
        pdb=" O   VAL B 512 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B 513 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1881 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1233
        2.75 -     3.29: 9288
        3.29 -     3.83: 15432
        3.83 -     4.36: 17584
        4.36 -     4.90: 32591
  Nonbonded interactions: 76128
  Sorted by model distance:
  nonbonded pdb=" OG  SER M 127 "
            pdb=" NZ  LYS I 218 "
     model   vdw
     2.218 3.120
  nonbonded pdb=" OG  SER M 120 "
            pdb=" OD1 ASN M 143 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" OG  SER L 120 "
            pdb=" OD1 ASN L 143 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" NZ  LYS H 218 "
            pdb=" OG  SER L 127 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" O   LEU H 174 "
            pdb=" CD1 LEU H 174 "
     model   vdw
     2.418 3.460
  ... (remaining 76123 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.930
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10890  Z= 0.187
  Angle     :  0.812   8.411  14830  Z= 0.437
  Chirality :  0.050   0.173   1652
  Planarity :  0.005   0.051   1882
  Dihedral  : 14.013  89.368   3954
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.59 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.13 %
    Favored  : 93.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.97 (0.22), residues: 1318
  helix: -2.70 (0.69), residues: 52
  sheet:  0.16 (0.24), residues: 482
  loop : -2.31 (0.19), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 328 
 TYR   0.019   0.002   TYR B 351 
 PHE   0.017   0.002   PHE H  29 
 TRP   0.027   0.002   TRP H  83 
 HIS   0.002   0.001   HIS L 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10870)
  covalent geometry    : angle       0.80927 (14786)
  SS BOND              : bond        0.00529 (   16)
  SS BOND              : angle       1.17870 (   32)
  hydrogen bonds       : bond        0.14114 (  314)
  hydrogen bonds       : angle       8.09289 (  792)
  link_BETA1-4         : bond        0.00256 (    2)
  link_BETA1-4         : angle       1.30712 (    6)
  link_NAG-ASN         : bond        0.00025 (    2)
  link_NAG-ASN         : angle       2.39084 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 177
  time to evaluate  : 0.467 
Fit side-chains
REVERT: H  142 LEU cc_start: 0.7623 (pp) cc_final: 0.7406 (pp)
REVERT: L  132 LYS cc_start: 0.8278 (mttt) cc_final: 0.8055 (pttm)
REVERT: M   51 LYS cc_start: 0.8025 (mttt) cc_final: 0.7779 (tttm)
REVERT: M  132 LYS cc_start: 0.7935 (mttt) cc_final: 0.7720 (pttm)
REVERT: I    6 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8179 (mt0)
REVERT: I   38 ARG cc_start: 0.8999 (ptm-80) cc_final: 0.8687 (ptm-80)
REVERT: I  142 LEU cc_start: 0.7429 (pp) cc_final: 0.7228 (pp)
  outliers start: 8
  outliers final: 4
  residues processed: 179
  average time/residue: 0.1295
  time to fit residues: 30.9394
Evaluate side-chains
  121 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain I residue    6 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0170
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
H  77 ASN
L  44 GLN
L 106 GLN
A  49 HIS
A 271 GLN
A 493 GLN
B 271 GLN
B 493 GLN
M  44 GLN
M 106 GLN
I  77 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.135430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.119075 restraints weight = 16643.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120411 restraints weight = 13327.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121369 restraints weight = 11351.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121896 restraints weight = 10066.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121921 restraints weight = 9276.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10890  Z= 0.166
  Angle     :  0.695   8.310  14830  Z= 0.358
  Chirality :  0.047   0.147   1652
  Planarity :  0.005   0.041   1882
  Dihedral  :  6.220  59.066   1553
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.33 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.45 (0.22), residues: 1318
  helix: -3.64 (0.71), residues: 28
  sheet:  0.51 (0.23), residues: 514
  loop : -2.01 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 408 
 TYR   0.015   0.002   TYR I 180 
 PHE   0.018   0.002   PHE L 122 
 TRP   0.016   0.002   TRP I  83 
 HIS   0.004   0.001   HIS I 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (10870)
  covalent geometry    : angle       0.69317 (14786)
  SS BOND              : bond        0.00539 (   16)
  SS BOND              : angle       1.06275 (   32)
  hydrogen bonds       : bond        0.04097 (  314)
  hydrogen bonds       : angle       6.56243 (  792)
  link_BETA1-4         : bond        0.00094 (    2)
  link_BETA1-4         : angle       0.93477 (    6)
  link_NAG-ASN         : bond        0.00053 (    2)
  link_NAG-ASN         : angle       1.61160 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.415 
Fit side-chains
REVERT: H  142 LEU cc_start: 0.7500 (pp) cc_final: 0.7240 (pp)
REVERT: A  471 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4391 (tp30)
REVERT: B  471 GLU cc_start: 0.4835 (OUTLIER) cc_final: 0.4422 (tp30)
REVERT: B  489 TYR cc_start: 0.8761 (m-80) cc_final: 0.8492 (m-80)
REVERT: M  149 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: I  142 LEU cc_start: 0.7445 (pp) cc_final: 0.7225 (pp)
  outliers start: 26
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1130
  time to fit residues: 20.6179
Evaluate side-chains
  118 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue    6 GLN
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 70 optimal weight:    0.4980
   chunk 92 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    9.9990
   chunk 126 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
A 493 GLN
B 493 GLN
I   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.133893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119798 restraints weight = 16784.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119805 restraints weight = 15906.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119962 restraints weight = 15004.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.120229 restraints weight = 14252.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120458 restraints weight = 13671.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10890  Z= 0.156
  Angle     :  0.636   8.149  14830  Z= 0.326
  Chirality :  0.046   0.150   1652
  Planarity :  0.005   0.043   1882
  Dihedral  :  5.578  55.276   1549
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.94 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.31 (0.22), residues: 1318
  helix: -4.19 (0.53), residues: 40
  sheet:  0.68 (0.23), residues: 514
  loop : -1.90 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 403 
 TYR   0.017   0.002   TYR I 180 
 PHE   0.016   0.002   PHE L 122 
 TRP   0.012   0.002   TRP B 436 
 HIS   0.004   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10870)
  covalent geometry    : angle       0.63439 (14786)
  SS BOND              : bond        0.00594 (   16)
  SS BOND              : angle       1.09649 (   32)
  hydrogen bonds       : bond        0.03835 (  314)
  hydrogen bonds       : angle       6.07079 (  792)
  link_BETA1-4         : bond        0.00284 (    2)
  link_BETA1-4         : angle       0.95444 (    6)
  link_NAG-ASN         : bond        0.00090 (    2)
  link_NAG-ASN         : angle       1.37311 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.413 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.5925 (ppp)
REVERT: H  142 LEU cc_start: 0.7414 (pp) cc_final: 0.7160 (pp)
REVERT: L  149 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7583 (tm-30)
REVERT: A  471 GLU cc_start: 0.5097 (OUTLIER) cc_final: 0.4598 (tp30)
REVERT: B  471 GLU cc_start: 0.5021 (OUTLIER) cc_final: 0.4607 (tp30)
REVERT: M  149 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: M  155 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6992 (mmmt)
REVERT: I   67 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7517 (mt0)
REVERT: I  142 LEU cc_start: 0.7511 (pp) cc_final: 0.7256 (pp)
  outliers start: 31
  outliers final: 19
  residues processed: 133
  average time/residue: 0.1079
  time to fit residues: 20.1326
Evaluate side-chains
  124 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 133 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 493 GLN
B 422 ASN
M   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.132087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.117375 restraints weight = 16980.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117697 restraints weight = 15894.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117872 restraints weight = 14367.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118125 restraints weight = 13739.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.118231 restraints weight = 13310.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10890  Z= 0.175
  Angle     :  0.646   8.109  14830  Z= 0.329
  Chirality :  0.046   0.156   1652
  Planarity :  0.004   0.043   1882
  Dihedral  :  5.271  40.161   1546
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 12.69 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.34 (0.22), residues: 1318
  helix: -4.28 (0.57), residues: 40
  sheet:  0.67 (0.23), residues: 514
  loop : -1.93 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  60 
 TYR   0.017   0.002   TYR I 180 
 PHE   0.019   0.002   PHE I 126 
 TRP   0.012   0.002   TRP B 436 
 HIS   0.004   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (10870)
  covalent geometry    : angle       0.64173 (14786)
  SS BOND              : bond        0.00612 (   16)
  SS BOND              : angle       1.67115 (   32)
  hydrogen bonds       : bond        0.03777 (  314)
  hydrogen bonds       : angle       5.96261 (  792)
  link_BETA1-4         : bond        0.00089 (    2)
  link_BETA1-4         : angle       0.76416 (    6)
  link_NAG-ASN         : bond        0.00054 (    2)
  link_NAG-ASN         : angle       1.40057 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 104
  time to evaluate  : 0.416 
Fit side-chains
REVERT: H  142 LEU cc_start: 0.7524 (pp) cc_final: 0.7294 (pp)
REVERT: L   31 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7227 (t80)
REVERT: L  114 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6967 (ptm160)
REVERT: L  149 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: A  471 GLU cc_start: 0.5082 (OUTLIER) cc_final: 0.4546 (tp30)
REVERT: B  471 GLU cc_start: 0.5067 (OUTLIER) cc_final: 0.4617 (tp30)
REVERT: M   31 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6547 (t80)
REVERT: M   51 LYS cc_start: 0.8122 (mttt) cc_final: 0.7805 (tttm)
REVERT: M  149 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7744 (tm-30)
REVERT: M  155 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6910 (mmmt)
REVERT: I    2 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6365 (ppp)
REVERT: I   67 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7691 (mt0)
REVERT: I  142 LEU cc_start: 0.7611 (pp) cc_final: 0.7358 (pp)
  outliers start: 43
  outliers final: 26
  residues processed: 140
  average time/residue: 0.1033
  time to fit residues: 20.7274
Evaluate side-chains
  130 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  440 ASN
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  184 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    3.9990
   chunk 128 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 125 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.129826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115116 restraints weight = 16931.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115255 restraints weight = 16142.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.115383 restraints weight = 14994.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.115547 restraints weight = 14659.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115607 restraints weight = 13966.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10890  Z= 0.214
  Angle     :  0.673   8.601  14830  Z= 0.344
  Chirality :  0.047   0.158   1652
  Planarity :  0.005   0.044   1882
  Dihedral  :  5.395  41.522   1546
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 13.87 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.47 (0.22), residues: 1318
  helix: -4.29 (0.65), residues: 40
  sheet:  0.63 (0.23), residues: 514
  loop : -2.06 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.020   0.002   TYR H 180 
 PHE   0.029   0.002   PHE H 126 
 TRP   0.012   0.002   TRP B 436 
 HIS   0.004   0.001   HIS I 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (10870)
  covalent geometry    : angle       0.66690 (14786)
  SS BOND              : bond        0.00733 (   16)
  SS BOND              : angle       1.88654 (   32)
  hydrogen bonds       : bond        0.04037 (  314)
  hydrogen bonds       : angle       6.04271 (  792)
  link_BETA1-4         : bond        0.00189 (    2)
  link_BETA1-4         : angle       0.86664 (    6)
  link_NAG-ASN         : bond        0.00031 (    2)
  link_NAG-ASN         : angle       1.45649 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 106
  time to evaluate  : 0.399 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6303 (ppp)
REVERT: H   67 GLN cc_start: 0.8671 (mm110) cc_final: 0.8432 (mm110)
REVERT: H  142 LEU cc_start: 0.7598 (pp) cc_final: 0.7377 (pp)
REVERT: L   31 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7155 (t80)
REVERT: L  114 ARG cc_start: 0.7260 (ptm-80) cc_final: 0.6953 (ptm160)
REVERT: L  149 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: A  471 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4628 (tp30)
REVERT: B  471 GLU cc_start: 0.5077 (OUTLIER) cc_final: 0.4611 (tp30)
REVERT: M   31 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.6474 (t80)
REVERT: M   51 LYS cc_start: 0.8188 (mttt) cc_final: 0.7816 (tttm)
REVERT: M  149 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7824 (tm-30)
REVERT: M  155 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6931 (mmmt)
REVERT: I    2 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6482 (ppp)
REVERT: I   16 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7438 (mt-10)
REVERT: I   67 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7691 (mt0)
REVERT: I  142 LEU cc_start: 0.7662 (pp) cc_final: 0.7416 (pp)
  outliers start: 50
  outliers final: 34
  residues processed: 149
  average time/residue: 0.1034
  time to fit residues: 22.0585
Evaluate side-chains
  138 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 123 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 119 optimal weight:    0.0770
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
H 196 GLN
A 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.131354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.116896 restraints weight = 16822.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.116952 restraints weight = 15930.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.117051 restraints weight = 14887.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117188 restraints weight = 14512.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117213 restraints weight = 13944.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10890  Z= 0.156
  Angle     :  0.634   8.925  14830  Z= 0.323
  Chirality :  0.046   0.209   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  5.311  40.383   1546
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.88 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.41 (0.22), residues: 1318
  helix: -4.07 (0.56), residues: 52
  sheet:  0.62 (0.23), residues: 522
  loop : -1.97 (0.20), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 457 
 TYR   0.014   0.001   TYR H 180 
 PHE   0.018   0.002   PHE H 126 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.003   0.001   HIS I 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10870)
  covalent geometry    : angle       0.63017 (14786)
  SS BOND              : bond        0.00836 (   16)
  SS BOND              : angle       1.45294 (   32)
  hydrogen bonds       : bond        0.03564 (  314)
  hydrogen bonds       : angle       5.88457 (  792)
  link_BETA1-4         : bond        0.00212 (    2)
  link_BETA1-4         : angle       0.77898 (    6)
  link_NAG-ASN         : bond        0.00130 (    2)
  link_NAG-ASN         : angle       1.35402 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 102
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: H    2 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6309 (ppp)
REVERT: H   67 GLN cc_start: 0.8645 (mm110) cc_final: 0.8385 (mm110)
REVERT: H  142 LEU cc_start: 0.7563 (pp) cc_final: 0.7345 (pp)
REVERT: L   31 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7129 (t80)
REVERT: L  114 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6895 (ptm160)
REVERT: L  149 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: L  155 LYS cc_start: 0.7257 (mmmt) cc_final: 0.6911 (mmmt)
REVERT: A  471 GLU cc_start: 0.5180 (OUTLIER) cc_final: 0.4665 (tp30)
REVERT: B  471 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.4679 (tp30)
REVERT: M   31 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.6469 (t80)
REVERT: M   51 LYS cc_start: 0.8174 (mttt) cc_final: 0.7796 (tttm)
REVERT: M  149 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7739 (tm-30)
REVERT: M  155 LYS cc_start: 0.7174 (mmmt) cc_final: 0.6850 (mmmt)
REVERT: I    2 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6337 (ppp)
REVERT: I   67 GLN cc_start: 0.8479 (mm-40) cc_final: 0.7703 (mt0)
REVERT: I  142 LEU cc_start: 0.7625 (pp) cc_final: 0.7383 (pp)
  outliers start: 46
  outliers final: 34
  residues processed: 141
  average time/residue: 0.1029
  time to fit residues: 20.7497
Evaluate side-chains
  139 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 99
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue  112 ILE
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   53 LEU
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 131 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
A 542 ASN
B 542 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.132394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117540 restraints weight = 16798.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117686 restraints weight = 15871.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.117893 restraints weight = 14586.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118239 restraints weight = 13744.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118302 restraints weight = 13167.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10890  Z= 0.140
  Angle     :  0.602   8.617  14830  Z= 0.307
  Chirality :  0.045   0.163   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  5.163  39.657   1546
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 16.05 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.26 (0.22), residues: 1318
  helix: -4.27 (0.61), residues: 40
  sheet:  0.72 (0.23), residues: 514
  loop : -1.86 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.012   0.001   TYR H 180 
 PHE   0.015   0.001   PHE H 126 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.002   0.001   HIS I 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10870)
  covalent geometry    : angle       0.59798 (14786)
  SS BOND              : bond        0.00618 (   16)
  SS BOND              : angle       1.41682 (   32)
  hydrogen bonds       : bond        0.03374 (  314)
  hydrogen bonds       : angle       5.67572 (  792)
  link_BETA1-4         : bond        0.00368 (    2)
  link_BETA1-4         : angle       0.88250 (    6)
  link_NAG-ASN         : bond        0.00115 (    2)
  link_NAG-ASN         : angle       1.33460 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 103
  time to evaluate  : 0.433 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6400 (ppp)
REVERT: H   67 GLN cc_start: 0.8635 (mm110) cc_final: 0.8354 (mm110)
REVERT: H  142 LEU cc_start: 0.7563 (pp) cc_final: 0.7353 (pp)
REVERT: L   31 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.6996 (t80)
REVERT: L  114 ARG cc_start: 0.7279 (ptm-80) cc_final: 0.6982 (ptm160)
REVERT: L  149 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: L  155 LYS cc_start: 0.7180 (mmmt) cc_final: 0.6873 (mmmt)
REVERT: A   41 LYS cc_start: 0.7879 (tppt) cc_final: 0.6951 (mtmm)
REVERT: A  471 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4400 (tp30)
REVERT: B   41 LYS cc_start: 0.7816 (tppt) cc_final: 0.6862 (mtmm)
REVERT: B  471 GLU cc_start: 0.4986 (OUTLIER) cc_final: 0.4456 (tp30)
REVERT: M   31 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.6431 (t80)
REVERT: M   51 LYS cc_start: 0.8174 (mttt) cc_final: 0.7801 (tttm)
REVERT: M  149 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: M  155 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6889 (mmmt)
REVERT: I    2 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6417 (ppp)
REVERT: I   67 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7697 (mt0)
REVERT: I  142 LEU cc_start: 0.7650 (pp) cc_final: 0.7421 (pp)
  outliers start: 51
  outliers final: 36
  residues processed: 147
  average time/residue: 0.1092
  time to fit residues: 22.5455
Evaluate side-chains
  144 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 102
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue  112 ILE
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   53 LEU
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue    5 VAL
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 70 optimal weight:    0.0030
   chunk 40 optimal weight:    0.0770
   chunk 78 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 112 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.3748

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.132725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.118315 restraints weight = 16519.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118615 restraints weight = 15349.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118694 restraints weight = 14214.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118897 restraints weight = 14070.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.119002 restraints weight = 13202.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10890  Z= 0.110
  Angle     :  0.571   8.261  14830  Z= 0.290
  Chirality :  0.044   0.162   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  4.972  38.352   1546
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 16.97 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.11 (0.23), residues: 1318
  helix: -4.44 (0.53), residues: 40
  sheet:  0.83 (0.23), residues: 514
  loop : -1.75 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 457 
 TYR   0.012   0.001   TYR L  55 
 PHE   0.010   0.001   PHE H 126 
 TRP   0.012   0.001   TRP A 436 
 HIS   0.001   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10870)
  covalent geometry    : angle       0.56800 (14786)
  SS BOND              : bond        0.00534 (   16)
  SS BOND              : angle       1.26316 (   32)
  hydrogen bonds       : bond        0.03054 (  314)
  hydrogen bonds       : angle       5.48944 (  792)
  link_BETA1-4         : bond        0.00427 (    2)
  link_BETA1-4         : angle       0.83798 (    6)
  link_NAG-ASN         : bond        0.00177 (    2)
  link_NAG-ASN         : angle       1.24096 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 100
  time to evaluate  : 0.456 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6392 (ppp)
REVERT: H   67 GLN cc_start: 0.8602 (mm110) cc_final: 0.7599 (mt0)
REVERT: H  142 LEU cc_start: 0.7522 (pp) cc_final: 0.7321 (pp)
REVERT: L   31 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6890 (t80)
REVERT: L  149 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: L  155 LYS cc_start: 0.7088 (mmmt) cc_final: 0.6827 (mmmt)
REVERT: A  471 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4574 (tp30)
REVERT: B  471 GLU cc_start: 0.4980 (OUTLIER) cc_final: 0.4570 (tp30)
REVERT: M   31 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6461 (t80)
REVERT: M  149 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: M  155 LYS cc_start: 0.7129 (mmmt) cc_final: 0.6896 (mmmt)
REVERT: I    2 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6476 (ppp)
REVERT: I   67 GLN cc_start: 0.8439 (mm-40) cc_final: 0.7692 (mt0)
  outliers start: 46
  outliers final: 35
  residues processed: 136
  average time/residue: 0.1085
  time to fit residues: 21.1418
Evaluate side-chains
  140 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue  112 ILE
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   chunk 126 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.130484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.115958 restraints weight = 16919.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.116134 restraints weight = 15526.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.116333 restraints weight = 14223.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.116560 restraints weight = 13724.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.116629 restraints weight = 13263.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10890  Z= 0.179
  Angle     :  0.628   8.672  14830  Z= 0.321
  Chirality :  0.046   0.163   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  5.190  40.024   1546
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.89 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.24 (0.22), residues: 1318
  helix: -4.50 (0.53), residues: 40
  sheet:  0.73 (0.23), residues: 514
  loop : -1.84 (0.20), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 457 
 TYR   0.015   0.002   TYR H 180 
 PHE   0.018   0.002   PHE H 126 
 TRP   0.011   0.001   TRP B 436 
 HIS   0.003   0.001   HIS I 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10870)
  covalent geometry    : angle       0.62285 (14786)
  SS BOND              : bond        0.00723 (   16)
  SS BOND              : angle       1.72398 (   32)
  hydrogen bonds       : bond        0.03596 (  314)
  hydrogen bonds       : angle       5.60621 (  792)
  link_BETA1-4         : bond        0.00265 (    2)
  link_BETA1-4         : angle       0.98854 (    6)
  link_NAG-ASN         : bond        0.00039 (    2)
  link_NAG-ASN         : angle       1.38093 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 104
  time to evaluate  : 0.436 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.6499 (ppp)
REVERT: H  142 LEU cc_start: 0.7591 (pp) cc_final: 0.7379 (pp)
REVERT: L   31 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.6765 (t80)
REVERT: L  149 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: L  155 LYS cc_start: 0.7163 (mmmt) cc_final: 0.6888 (mmmt)
REVERT: A  471 GLU cc_start: 0.4983 (OUTLIER) cc_final: 0.4470 (tp30)
REVERT: B  471 GLU cc_start: 0.4970 (OUTLIER) cc_final: 0.4448 (tp30)
REVERT: M   31 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6276 (t80)
REVERT: M   51 LYS cc_start: 0.8269 (mttt) cc_final: 0.7830 (tttm)
REVERT: M  149 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: M  155 LYS cc_start: 0.7183 (mmmt) cc_final: 0.6935 (mmmt)
REVERT: I    2 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6582 (ppp)
REVERT: I   67 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7704 (mt0)
REVERT: I  142 LEU cc_start: 0.7698 (pp) cc_final: 0.7481 (pp)
  outliers start: 48
  outliers final: 41
  residues processed: 143
  average time/residue: 0.1108
  time to fit residues: 22.4439
Evaluate side-chains
  145 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 98
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   78 THR
Chi-restraints excluded: chain L residue  112 ILE
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  350 VAL
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   53 LEU
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0670
   chunk 47 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.5130

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120134 restraints weight = 16519.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119914 restraints weight = 14796.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.120060 restraints weight = 13494.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.120326 restraints weight = 13431.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.120413 restraints weight = 12425.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10890  Z= 0.131
  Angle     :  0.604   8.552  14830  Z= 0.307
  Chirality :  0.044   0.161   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  5.095  39.066   1546
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 16.89 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.15 (0.23), residues: 1318
  helix: -4.41 (0.55), residues: 40
  sheet:  0.84 (0.23), residues: 510
  loop : -1.81 (0.21), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 457 
 TYR   0.013   0.001   TYR A 495 
 PHE   0.013   0.001   PHE H 126 
 TRP   0.012   0.001   TRP B 436 
 HIS   0.002   0.001   HIS I 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10870)
  covalent geometry    : angle       0.59926 (14786)
  SS BOND              : bond        0.00622 (   16)
  SS BOND              : angle       1.67800 (   32)
  hydrogen bonds       : bond        0.03183 (  314)
  hydrogen bonds       : angle       5.50952 (  792)
  link_BETA1-4         : bond        0.00367 (    2)
  link_BETA1-4         : angle       0.89185 (    6)
  link_NAG-ASN         : bond        0.00142 (    2)
  link_NAG-ASN         : angle       1.29646 (    6)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 0.419 
Fit side-chains
REVERT: H    2 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6498 (ppp)
REVERT: H   67 GLN cc_start: 0.8677 (mm110) cc_final: 0.7644 (mt0)
REVERT: H  142 LEU cc_start: 0.7596 (pp) cc_final: 0.7374 (pp)
REVERT: L   31 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6605 (t80)
REVERT: L  149 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: L  155 LYS cc_start: 0.7121 (mmmt) cc_final: 0.6874 (mmmt)
REVERT: A  471 GLU cc_start: 0.4778 (OUTLIER) cc_final: 0.4348 (tp30)
REVERT: B  471 GLU cc_start: 0.4864 (OUTLIER) cc_final: 0.4327 (tp30)
REVERT: M   31 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.6229 (t80)
REVERT: M   51 LYS cc_start: 0.8215 (mttt) cc_final: 0.7710 (tttm)
REVERT: M  149 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7690 (tm-30)
REVERT: M  155 LYS cc_start: 0.7162 (mmmt) cc_final: 0.6952 (mmmt)
REVERT: I    2 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6527 (ppp)
REVERT: I   67 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7680 (mt0)
REVERT: I  142 LEU cc_start: 0.7656 (pp) cc_final: 0.7418 (pp)
  outliers start: 48
  outliers final: 41
  residues processed: 144
  average time/residue: 0.0989
  time to fit residues: 20.4421
Evaluate side-chains
  146 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 99
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 MET
Chi-restraints excluded: chain H residue   31 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  125 VAL
Chi-restraints excluded: chain H residue  154 VAL
Chi-restraints excluded: chain H residue  173 VAL
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  183 SER
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  185 VAL
Chi-restraints excluded: chain H residue  201 ASN
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   31 TYR
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue  112 ILE
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  121 VAL
Chi-restraints excluded: chain L residue  181 LEU
Chi-restraints excluded: chain L residue  215 PHE
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  480 CYS
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain M residue    2 ILE
Chi-restraints excluded: chain M residue   31 TYR
Chi-restraints excluded: chain M residue   53 LEU
Chi-restraints excluded: chain M residue   78 THR
Chi-restraints excluded: chain M residue  116 VAL
Chi-restraints excluded: chain M residue  121 VAL
Chi-restraints excluded: chain M residue  181 LEU
Chi-restraints excluded: chain M residue  215 PHE
Chi-restraints excluded: chain I residue    2 MET
Chi-restraints excluded: chain I residue   31 THR
Chi-restraints excluded: chain I residue   78 THR
Chi-restraints excluded: chain I residue  104 THR
Chi-restraints excluded: chain I residue  125 VAL
Chi-restraints excluded: chain I residue  173 VAL
Chi-restraints excluded: chain I residue  179 LEU
Chi-restraints excluded: chain I residue  184 SER
Chi-restraints excluded: chain I residue  185 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 126 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0270
   chunk 92 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.9844

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.131980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117117 restraints weight = 16801.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117579 restraints weight = 15079.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117932 restraints weight = 13180.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118310 restraints weight = 12613.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.118519 restraints weight = 11864.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10890  Z= 0.203
  Angle     :  0.658   9.153  14830  Z= 0.336
  Chirality :  0.046   0.163   1652
  Planarity :  0.004   0.044   1882
  Dihedral  :  5.301  40.909   1546
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.81 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.30 (0.22), residues: 1318
  helix: -4.40 (0.57), residues: 40
  sheet:  0.66 (0.23), residues: 526
  loop : -1.90 (0.21), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 457 
 TYR   0.017   0.002   TYR H 180 
 PHE   0.020   0.002   PHE H 126 
 TRP   0.010   0.001   TRP B 436 
 HIS   0.003   0.001   HIS H 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (10870)
  covalent geometry    : angle       0.65209 (14786)
  SS BOND              : bond        0.00715 (   16)
  SS BOND              : angle       1.86232 (   32)
  hydrogen bonds       : bond        0.03773 (  314)
  hydrogen bonds       : angle       5.65980 (  792)
  link_BETA1-4         : bond        0.00201 (    2)
  link_BETA1-4         : angle       1.01087 (    6)
  link_NAG-ASN         : bond        0.00019 (    2)
  link_NAG-ASN         : angle       1.50711 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1728.60 seconds
wall clock time: 30 minutes 41.36 seconds (1841.36 seconds total)