Starting phenix.real_space_refine
on Thu Mar  5 00:14:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oz6_71049/03_2026/9oz6_71049_trim.cif"
  }
  resolution = 2.7
  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=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5495      2.51       5
     N    1388      2.21       5
     O    1640      1.98       5
     H    8071      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 16635
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 652
          Classifications: {'peptide': 41}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
    Chain: "B"
      Number of atoms: 15857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1013, 15857
          Classifications: {'peptide': 1013}
          Link IDs: {'PTRANS': 51, 'TRANS': 961}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 126
          Unusual residues: {'NAG': 9}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 9
  Time building chain proxies: 2.61, per 1000 atoms: 0.16
  Number of scatterers: 16635
  At special positions: 0
  Unit cell: (91.728, 145.08, 111.384, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     O    1640      8.00
     N    1388      7.00
     C    5495      6.00
     H    8071      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  30 " - pdb=" SG  CYS B  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  57 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B  84 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  76 " - pdb=" SG  CYS B  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 324 " - pdb=" SG  CYS B 546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 401 " - pdb=" SG  CYS B 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 864 " - pdb=" SG  CYS B 868 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 984 " - pdb=" SG  CYS B1000 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B2401 " - " ASN B 123 "
      " NAG B2402 " - " ASN B 132 "
      " NAG B2403 " - " ASN B 333 "
      " NAG B2404 " - " ASN B 405 "
      " NAG B2405 " - " ASN B 480 "
      " NAG B2406 " - " ASN B 607 "
      " NAG B2407 " - " ASN B 628 "
      " NAG B2408 " - " ASN B 971 "
      " NAG B2409 " - " ASN B  49 "
  Time building additional restraints: 1.55
  Conformation dependent library (CDL) restraints added in 478.8 milliseconds
  

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1994

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 24 sheets defined
      8.0% alpha, 42.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 38
    Processing helix  chain 'B' and resid 49 through 64
      removed outlier: 3.546A  pdb=" N   TRP B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 70
      No H-bonds generated for 'chain 'B' and resid 68 through 70'
    Processing helix  chain 'B' and resid 71 through 80
    Processing helix  chain 'B' and resid 82 through 108
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 364 through 368
    Processing helix  chain 'B' and resid 563 through 567
    Processing helix  chain 'B' and resid 931 through 935
    Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 336
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350
      removed outlier: 7.104A  pdb=" N   MET A 366 " --> pdb=" O   GLU B 541 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   VAL B 526 " --> pdb=" O   TYR B 542 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   PHE B 518 " --> pdb=" O   GLU B 529 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42
      removed outlier: 6.848A  pdb=" N   GLU B  41 " --> pdb=" O   VAL B 782 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   ALA B 784 " --> pdb=" O   GLU B  41 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ILE B 770 " --> pdb=" O   VAL B 783 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET B 751 " --> pdb=" O   ALA B 764 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 119
      removed outlier: 6.761A  pdb=" N   THR B 125 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 157
      removed outlier: 5.580A  pdb=" N   TYR B 153 " --> pdb=" O   TRP B 142 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   TRP B 142 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU B 155 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ILE B 140 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 152 through 157
      removed outlier: 5.580A  pdb=" N   TYR B 153 " --> pdb=" O   TRP B 142 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   TRP B 142 " --> pdb=" O   TYR B 153 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU B 155 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ILE B 140 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 208 through 216
      removed outlier: 5.428A  pdb=" N   ILE B 209 " --> pdb=" O   PHE B 225 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   PHE B 225 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP B 211 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   SER B 215 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   THR B 219 " --> pdb=" O   SER B 215 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 252
      removed outlier: 4.957A  pdb=" N   VAL B 275 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   TYR B 237 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 237 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 239 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU B 241 " --> pdb=" O   ARG B 269 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ARG B 269 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 247 through 252
      removed outlier: 4.957A  pdb=" N   VAL B 275 " --> pdb=" O   VAL B 235 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   TYR B 237 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 237 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU B 239 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU B 241 " --> pdb=" O   ARG B 269 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ARG B 269 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 324
      removed outlier: 3.888A  pdb=" N   TRP B 301 " --> pdb=" O   TYR B 562 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   SER B 305 " --> pdb=" O   ASN B 558 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   ASN B 558 " --> pdb=" O   SER B 305 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 334 through 340
      removed outlier: 3.801A  pdb=" N   GLY B 336 " --> pdb=" O   SER B 349 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 345 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ILE B 354 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 384
      removed outlier: 3.868A  pdb=" N   SER B 380 " --> pdb=" O   VAL B 393 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 422 through 426
      removed outlier: 3.869A  pdb=" N   LYS B 422 " --> pdb=" O   LEU B 435 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 440 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 470
      removed outlier: 6.508A  pdb=" N   PHE B 486 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 576 through 582
      removed outlier: 5.657A  pdb=" N   LEU B 577 " --> pdb=" O   SER B 592 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   SER B 592 " --> pdb=" O   LEU B 577 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 623 through 629
      removed outlier: 3.563A  pdb=" N   ASN B 628 " --> pdb=" O   TYR B 610 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   TYR B 610 " --> pdb=" O   ASN B 628 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 623 through 629
      removed outlier: 3.563A  pdb=" N   ASN B 628 " --> pdb=" O   TYR B 610 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   TYR B 610 " --> pdb=" O   ASN B 628 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 698 through 701
      removed outlier: 5.626A  pdb=" N   PHE B 699 " --> pdb=" O   LYS B 688 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LYS B 688 " --> pdb=" O   PHE B 699 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA B 926 " --> pdb=" O   VAL B 681 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 710 through 713
    Processing sheet with id=AC2, first strand: chain 'B' and resid 790 through 796
      removed outlier: 3.755A  pdb=" N   THR B 809 " --> pdb=" O   THR B 806 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   VAL B 810 " --> pdb=" O   LEU B 823 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 832 through 840
      removed outlier: 6.877A  pdb=" N   LEU B 849 " --> pdb=" O   VAL B 835 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   LEU B 837 " --> pdb=" O   TYR B 847 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   TYR B 847 " --> pdb=" O   LEU B 837 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   LEU B 839 " --> pdb=" O   PHE B 845 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   PHE B 845 " --> pdb=" O   LEU B 839 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   LEU B 858 " --> pdb=" O   ALA B 878 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   ALA B 878 " --> pdb=" O   LEU B 858 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   ARG B 860 " --> pdb=" O   ILE B 876 " (cutoff:3.500A)
      removed outlier: 8.103A  pdb=" N   ILE B 876 " --> pdb=" O   ARG B 860 " (cutoff:3.500A)
      removed outlier: 8.594A  pdb=" N   SER B 862 " --> pdb=" O   THR B 874 " (cutoff:3.500A)
      removed outlier: 9.483A  pdb=" N   THR B 874 " --> pdb=" O   SER B 862 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 884 through 891
      removed outlier: 6.722A  pdb=" N   ALA B 888 " --> pdb=" O   ILE B 899 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ILE B 899 " --> pdb=" O   ALA B 888 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 958 through 960
    Processing sheet with id=AC6, first strand: chain 'B' and resid 982 through 986

    322 hydrogen bonds defined for protein.
    834 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: 4.06

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8067
        1.03 -     1.23: 130
        1.23 -     1.43: 3778
        1.43 -     1.62: 4847
        1.62 -     1.82: 56
  Bond restraints: 16878
  Sorted by residual:
  bond pdb=" N   CYS B  24 "
       pdb=" CA  CYS B  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  bond pdb=" N   CYS B  24 "
       pdb=" H   CYS B  24 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" CA  ILE A 369 "
       pdb=" CB  ILE A 369 "
    ideal  model  delta    sigma   weight residual
    1.546  1.537  0.010 8.80e-03 1.29e+04 1.20e+00
  bond pdb=" N   GLY B 583 "
       pdb=" CA  GLY B 583 "
    ideal  model  delta    sigma   weight residual
    1.449  1.435  0.014 1.45e-02 4.76e+03 9.19e-01
  bond pdb=" CA  LEU B 491 "
       pdb=" C   LEU B 491 "
    ideal  model  delta    sigma   weight residual
    1.523  1.510  0.013 1.34e-02 5.57e+03 9.04e-01
  ... (remaining 16873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 28483
        1.03 -     2.05: 1673
        2.05 -     3.08: 94
        3.08 -     4.11: 42
        4.11 -     5.13: 9
  Bond angle restraints: 30301
  Sorted by residual:
  angle pdb=" N   LYS B 865 "
        pdb=" CA  LYS B 865 "
        pdb=" C   LYS B 865 "
      ideal   model   delta    sigma   weight residual
     112.13  107.88    4.25 1.37e+00 5.33e-01 9.61e+00
  angle pdb=" CA  ASN B 706 "
        pdb=" C   ASN B 706 "
        pdb=" N   ILE B 707 "
      ideal   model   delta    sigma   weight residual
     114.59  118.42   -3.83 1.48e+00 4.57e-01 6.70e+00
  angle pdb=" N   SER B 200 "
        pdb=" CA  SER B 200 "
        pdb=" C   SER B 200 "
      ideal   model   delta    sigma   weight residual
     107.93  112.10   -4.17 1.65e+00 3.67e-01 6.39e+00
  angle pdb=" N   ASN B 768 "
        pdb=" CA  ASN B 768 "
        pdb=" C   ASN B 768 "
      ideal   model   delta    sigma   weight residual
     110.61  107.49    3.12 1.25e+00 6.40e-01 6.22e+00
  angle pdb=" N   GLY B1033 "
        pdb=" CA  GLY B1033 "
        pdb=" C   GLY B1033 "
      ideal   model   delta    sigma   weight residual
     110.63  114.23   -3.60 1.45e+00 4.76e-01 6.17e+00
  ... (remaining 30296 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 7713
       17.90 -    35.80: 367
       35.80 -    53.71: 114
       53.71 -    71.61: 39
       71.61 -    89.51: 5
  Dihedral angle restraints: 8238
    sinusoidal: 4383
      harmonic: 3855
  Sorted by residual:
  dihedral pdb=" CB  CYS A 334 "
           pdb=" SG  CYS A 334 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -143.15   57.15     1      1.00e+01 1.00e-02 4.39e+01
  dihedral pdb=" CB  CYS B  72 "
           pdb=" SG  CYS B  72 "
           pdb=" SG  CYS B  93 "
           pdb=" CB  CYS B  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.83  -39.83     1      1.00e+01 1.00e-02 2.23e+01
  dihedral pdb=" CA  PRO B 449 "
           pdb=" C   PRO B 449 "
           pdb=" N   ASP B 450 "
           pdb=" CA  ASP B 450 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.51  -19.49     0      5.00e+00 4.00e-02 1.52e+01
  ... (remaining 8235 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 765
       0.028 -    0.056: 382
       0.056 -    0.084: 64
       0.084 -    0.111: 92
       0.111 -    0.139: 30
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" CA  VAL B1008 "
            pdb=" N   VAL B1008 "
            pdb=" C   VAL B1008 "
            pdb=" CB  VAL B1008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  ILE B 704 "
            pdb=" N   ILE B 704 "
            pdb=" C   ILE B 704 "
            pdb=" CB  ILE B 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  VAL B 503 "
            pdb=" N   VAL B 503 "
            pdb=" C   VAL B 503 "
            pdb=" CB  VAL B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.27e-01
  ... (remaining 1330 not shown)

  Planarity restraints: 2526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 701 "    0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO B 702 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 702 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 702 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 448 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.90e+00
        pdb=" N   PRO B 449 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 282 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO B 283 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 283 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 283 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2523 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 491
        2.15 -     2.76: 31014
        2.76 -     3.37: 45387
        3.37 -     3.99: 63095
        3.99 -     4.60: 96633
  Nonbonded interactions: 236620
  Sorted by model distance:
  nonbonded pdb=" HH  TYR A 341 "
            pdb=" OE1 GLU A 347 "
     model   vdw
     1.536 2.450
  nonbonded pdb=" O   TRP B 712 "
            pdb=" HZ1 LYS B 935 "
     model   vdw
     1.574 2.450
  nonbonded pdb="HH22 ARG B 311 "
            pdb=" OE1 GLU B 552 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" O   PRO B 449 "
            pdb=" H   THR B 451 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" HD1 HIS B 145 "
            pdb=" OE2 GLU B 174 "
     model   vdw
     1.612 2.450
  ... (remaining 236615 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.100
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     15.790
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
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   0.032   8827  Z= 0.176
  Angle     :  0.549   5.134  12053  Z= 0.308
  Chirality :  0.043   0.139   1333
  Planarity :  0.003   0.036   1519
  Dihedral  : 10.375  89.511   3256
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.24 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.27), residues: 1046
  helix:  3.46 (0.69), residues: 62
  sheet:  0.15 (0.24), residues: 437
  loop : -0.48 (0.28), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 475 
 TYR   0.009   0.001   TYR B 513 
 PHE   0.010   0.001   PHE B 918 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 8807)
  covalent geometry    : angle       0.53809 (12004)
  SS BOND              : bond        0.00237 (   11)
  SS BOND              : angle       0.82113 (   22)
  hydrogen bonds       : bond        0.18728 (  293)
  hydrogen bonds       : angle       8.37655 (  834)
  link_NAG-ASN         : bond        0.00249 (    9)
  link_NAG-ASN         : angle       2.29523 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8362 (tp40) cc_final: 0.8022 (tp-100)
REVERT: B  260 TYR cc_start: 0.8693 (t80) cc_final: 0.8404 (t80)
REVERT: B  327 ASN cc_start: 0.8958 (m110) cc_final: 0.8729 (m-40)
REVERT: B  394 MET cc_start: 0.8668 (ttp) cc_final: 0.8432 (ttp)
REVERT: B  495 GLU cc_start: 0.7567 (tp30) cc_final: 0.7063 (tp30)
REVERT: B  547 SER cc_start: 0.8535 (m) cc_final: 0.8204 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 77
  average time/residue: 1.3358
  time to fit residues: 108.9402
Evaluate side-chains
  58 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN
B 516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.100344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.072076 restraints weight = 40803.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.46
r_work: 0.2926 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.0923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8827  Z= 0.232
  Angle     :  0.586   7.992  12053  Z= 0.310
  Chirality :  0.046   0.159   1333
  Planarity :  0.004   0.045   1519
  Dihedral  :  5.167  30.327   1329
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  6.18 %
    Favored  : 93.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.26), residues: 1046
  helix:  3.46 (0.66), residues: 63
  sheet: -0.15 (0.24), residues: 440
  loop : -0.52 (0.28), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 901 
 TYR   0.011   0.001   TYR B 677 
 PHE   0.012   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 8807)
  covalent geometry    : angle       0.57451 (12004)
  SS BOND              : bond        0.00435 (   11)
  SS BOND              : angle       1.42636 (   22)
  hydrogen bonds       : bond        0.05448 (  293)
  hydrogen bonds       : angle       6.10235 (  834)
  link_NAG-ASN         : bond        0.00338 (    9)
  link_NAG-ASN         : angle       2.21294 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7517 (tm-30)
REVERT: B   31 GLN cc_start: 0.8216 (tp40) cc_final: 0.7827 (tp40)
REVERT: B  210 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7960 (mtpt)
REVERT: B  314 TYR cc_start: 0.8355 (t80) cc_final: 0.8129 (t80)
REVERT: B  495 GLU cc_start: 0.7736 (tp30) cc_final: 0.7289 (tp30)
REVERT: B  547 SER cc_start: 0.8410 (m) cc_final: 0.8108 (t)
  outliers start: 4
  outliers final: 0
  residues processed: 64
  average time/residue: 1.4224
  time to fit residues: 96.6675
Evaluate side-chains
  57 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  210 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 81 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 497 HIS
B 516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.100346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.072318 restraints weight = 41118.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.44
r_work: 0.2944 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8827  Z= 0.163
  Angle     :  0.537   8.321  12053  Z= 0.279
  Chirality :  0.045   0.146   1333
  Planarity :  0.004   0.041   1519
  Dihedral  :  5.079  27.829   1329
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  6.40 %
    Favored  : 93.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.34 (0.26), residues: 1046
  helix:  3.73 (0.67), residues: 63
  sheet: -0.27 (0.23), residues: 439
  loop : -0.60 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 901 
 TYR   0.011   0.001   TYR B 237 
 PHE   0.010   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 8807)
  covalent geometry    : angle       0.52650 (12004)
  SS BOND              : bond        0.00314 (   11)
  SS BOND              : angle       1.41958 (   22)
  hydrogen bonds       : bond        0.04302 (  293)
  hydrogen bonds       : angle       5.55444 (  834)
  link_NAG-ASN         : bond        0.00221 (    9)
  link_NAG-ASN         : angle       2.00718 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: B   31 GLN cc_start: 0.8144 (tp40) cc_final: 0.7775 (tp40)
REVERT: B  210 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8016 (mtpt)
REVERT: B  495 GLU cc_start: 0.7781 (tp30) cc_final: 0.7360 (tp30)
  outliers start: 5
  outliers final: 1
  residues processed: 64
  average time/residue: 1.4408
  time to fit residues: 97.6856
Evaluate side-chains
  59 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  210 LYS
Chi-restraints excluded: chain B residue  352 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.099868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.071335 restraints weight = 41036.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.47
r_work: 0.2932 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8827  Z= 0.200
  Angle     :  0.541   8.218  12053  Z= 0.280
  Chirality :  0.045   0.153   1333
  Planarity :  0.004   0.070   1519
  Dihedral  :  5.106  28.579   1329
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.36 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.26), residues: 1046
  helix:  3.74 (0.67), residues: 63
  sheet: -0.39 (0.23), residues: 439
  loop : -0.67 (0.28), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 901 
 TYR   0.010   0.001   TYR B 677 
 PHE   0.008   0.001   PHE B1024 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 8807)
  covalent geometry    : angle       0.52989 (12004)
  SS BOND              : bond        0.00301 (   11)
  SS BOND              : angle       1.34707 (   22)
  hydrogen bonds       : bond        0.04025 (  293)
  hydrogen bonds       : angle       5.38521 (  834)
  link_NAG-ASN         : bond        0.00291 (    9)
  link_NAG-ASN         : angle       2.05424 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  347 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: B   31 GLN cc_start: 0.8143 (tp40) cc_final: 0.7755 (tp40)
REVERT: B  210 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7977 (mtpt)
REVERT: B  352 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8181 (p0)
REVERT: B  495 GLU cc_start: 0.7856 (tp30) cc_final: 0.7409 (tp30)
  outliers start: 6
  outliers final: 1
  residues processed: 62
  average time/residue: 1.4472
  time to fit residues: 94.9378
Evaluate side-chains
  60 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  210 LYS
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  352 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 9 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN
B 516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.101018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.072966 restraints weight = 40785.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.46
r_work: 0.2951 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8827  Z= 0.141
  Angle     :  0.514   8.213  12053  Z= 0.266
  Chirality :  0.045   0.152   1333
  Planarity :  0.004   0.077   1519
  Dihedral  :  4.949  27.899   1329
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.25 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 1046
  helix:  4.03 (0.66), residues: 62
  sheet: -0.36 (0.23), residues: 434
  loop : -0.65 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 901 
 TYR   0.010   0.001   TYR B 677 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8807)
  covalent geometry    : angle       0.50548 (12004)
  SS BOND              : bond        0.00283 (   11)
  SS BOND              : angle       1.10658 (   22)
  hydrogen bonds       : bond        0.03650 (  293)
  hydrogen bonds       : angle       5.21767 (  834)
  link_NAG-ASN         : bond        0.00198 (    9)
  link_NAG-ASN         : angle       1.85986 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8100 (tp40) cc_final: 0.7702 (tp40)
REVERT: B  210 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7977 (mtpt)
REVERT: B  352 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8200 (p0)
REVERT: B  495 GLU cc_start: 0.7838 (tp30) cc_final: 0.7402 (tp30)
  outliers start: 7
  outliers final: 1
  residues processed: 63
  average time/residue: 1.4286
  time to fit residues: 95.4774
Evaluate side-chains
  59 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  210 LYS
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  352 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 146 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.100708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.072553 restraints weight = 40684.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3029 rms_B_bonded: 2.46
r_work: 0.2943 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8827  Z= 0.179
  Angle     :  0.522   8.121  12053  Z= 0.270
  Chirality :  0.045   0.152   1333
  Planarity :  0.004   0.083   1519
  Dihedral  :  4.978  28.920   1329
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.57 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.26), residues: 1046
  helix:  3.87 (0.66), residues: 63
  sheet: -0.45 (0.23), residues: 440
  loop : -0.67 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 901 
 TYR   0.009   0.001   TYR B 677 
 PHE   0.008   0.001   PHE B 754 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 8807)
  covalent geometry    : angle       0.51272 (12004)
  SS BOND              : bond        0.00251 (   11)
  SS BOND              : angle       1.25480 (   22)
  hydrogen bonds       : bond        0.03684 (  293)
  hydrogen bonds       : angle       5.16044 (  834)
  link_NAG-ASN         : bond        0.00253 (    9)
  link_NAG-ASN         : angle       1.91292 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: B   31 GLN cc_start: 0.8119 (tp40) cc_final: 0.7710 (tp40)
REVERT: B  146 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8515 (mm-40)
REVERT: B  210 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7966 (mtpt)
REVERT: B  352 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8251 (p0)
REVERT: B  495 GLU cc_start: 0.7869 (tp30) cc_final: 0.7415 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 64
  average time/residue: 1.3928
  time to fit residues: 94.6111
Evaluate side-chains
  63 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 GLN
Chi-restraints excluded: chain B residue  210 LYS
Chi-restraints excluded: chain B residue  244 GLU
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  352 ASN
Chi-restraints excluded: chain B residue  545 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 104 optimal weight:    0.1980
   chunk 17 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 94 optimal weight:    0.2980
   chunk 97 optimal weight:    0.5980
   chunk 100 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.3878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.101428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.073672 restraints weight = 40758.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.43
r_work: 0.2962 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2859 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8827  Z= 0.115
  Angle     :  0.507   8.172  12053  Z= 0.261
  Chirality :  0.044   0.150   1333
  Planarity :  0.004   0.084   1519
  Dihedral  :  4.836  28.702   1329
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 1.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  7.57 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.26), residues: 1046
  helix:  3.98 (0.67), residues: 63
  sheet: -0.48 (0.23), residues: 443
  loop : -0.62 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 901 
 TYR   0.009   0.001   TYR B 237 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B 497 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8807)
  covalent geometry    : angle       0.49891 (12004)
  SS BOND              : bond        0.00196 (   11)
  SS BOND              : angle       1.04232 (   22)
  hydrogen bonds       : bond        0.03395 (  293)
  hydrogen bonds       : angle       5.06209 (  834)
  link_NAG-ASN         : bond        0.00175 (    9)
  link_NAG-ASN         : angle       1.73744 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 MET cc_start: 0.8339 (mmm) cc_final: 0.7878 (mmm)
REVERT: B   31 GLN cc_start: 0.8040 (tp40) cc_final: 0.7625 (tp40)
REVERT: B  210 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7948 (mtpt)
REVERT: B  483 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7293 (mm-30)
REVERT: B  495 GLU cc_start: 0.7859 (tp30) cc_final: 0.7402 (tp30)
REVERT: B  602 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8489 (mpt-90)
  outliers start: 5
  outliers final: 3
  residues processed: 64
  average time/residue: 1.6006
  time to fit residues: 108.0777
Evaluate side-chains
  60 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  210 LYS
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  545 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0020
   chunk 104 optimal weight:    0.0050
   chunk 48 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.3002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.095709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.067431 restraints weight = 38570.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.36
r_work: 0.2780 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2649 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8827  Z= 0.099
  Angle     :  0.491   7.919  12053  Z= 0.252
  Chirality :  0.044   0.146   1333
  Planarity :  0.004   0.096   1519
  Dihedral  :  4.599  27.029   1329
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  8.10 %
    Favored  : 91.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1046
  helix:  4.08 (0.67), residues: 63
  sheet: -0.46 (0.23), residues: 443
  loop : -0.57 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 901 
 TYR   0.008   0.001   TYR B 677 
 PHE   0.009   0.001   PHE B 225 
 TRP   0.012   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 8807)
  covalent geometry    : angle       0.48435 (12004)
  SS BOND              : bond        0.00157 (   11)
  SS BOND              : angle       0.98272 (   22)
  hydrogen bonds       : bond        0.03146 (  293)
  hydrogen bonds       : angle       4.89152 (  834)
  link_NAG-ASN         : bond        0.00160 (    9)
  link_NAG-ASN         : angle       1.55432 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 MET cc_start: 0.8491 (mmm) cc_final: 0.8156 (mmm)
REVERT: B  483 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7471 (mm-30)
REVERT: B  495 GLU cc_start: 0.7877 (tp30) cc_final: 0.7506 (tp30)
REVERT: B  602 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8503 (mpt-90)
  outliers start: 2
  outliers final: 2
  residues processed: 60
  average time/residue: 1.4821
  time to fit residues: 94.0741
Evaluate side-chains
  59 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  545 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0980
   chunk 47 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 89 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.096466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.067393 restraints weight = 37972.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 2.38
r_work: 0.2767 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8827  Z= 0.127
  Angle     :  0.497   7.894  12053  Z= 0.255
  Chirality :  0.044   0.146   1333
  Planarity :  0.004   0.094   1519
  Dihedral  :  4.580  26.685   1329
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.10 %
    Favored  : 91.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.41 (0.26), residues: 1046
  helix:  4.05 (0.67), residues: 63
  sheet: -0.45 (0.23), residues: 443
  loop : -0.56 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 901 
 TYR   0.008   0.001   TYR B 677 
 PHE   0.008   0.001   PHE B 225 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.002   0.001   HIS B1004 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8807)
  covalent geometry    : angle       0.49022 (12004)
  SS BOND              : bond        0.00189 (   11)
  SS BOND              : angle       0.98749 (   22)
  hydrogen bonds       : bond        0.03237 (  293)
  hydrogen bonds       : angle       4.86742 (  834)
  link_NAG-ASN         : bond        0.00168 (    9)
  link_NAG-ASN         : angle       1.56643 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 MET cc_start: 0.8516 (mmm) cc_final: 0.8181 (mmm)
REVERT: B  483 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7514 (mm-30)
REVERT: B  495 GLU cc_start: 0.7895 (tp30) cc_final: 0.7522 (tp30)
REVERT: B  602 ARG cc_start: 0.8741 (mmm160) cc_final: 0.8493 (mpt-90)
  outliers start: 3
  outliers final: 3
  residues processed: 61
  average time/residue: 1.5380
  time to fit residues: 99.0471
Evaluate side-chains
  57 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  545 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 94 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.100600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.072588 restraints weight = 40994.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 2.43
r_work: 0.2952 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8827  Z= 0.173
  Angle     :  0.517   9.229  12053  Z= 0.265
  Chirality :  0.044   0.151   1333
  Planarity :  0.004   0.098   1519
  Dihedral  :  4.724  28.188   1329
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.42 %
    Favored  : 91.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.46 (0.26), residues: 1046
  helix:  4.00 (0.66), residues: 63
  sheet: -0.46 (0.23), residues: 439
  loop : -0.61 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 901 
 TYR   0.010   0.001   TYR B 677 
 PHE   0.009   0.001   PHE B 754 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 8807)
  covalent geometry    : angle       0.51012 (12004)
  SS BOND              : bond        0.00240 (   11)
  SS BOND              : angle       1.05102 (   22)
  hydrogen bonds       : bond        0.03444 (  293)
  hydrogen bonds       : angle       4.91943 (  834)
  link_NAG-ASN         : bond        0.00226 (    9)
  link_NAG-ASN         : angle       1.67009 (   27)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  366 MET cc_start: 0.8353 (mmm) cc_final: 0.7947 (mmm)
REVERT: B  421 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7952 (mpp80)
REVERT: B  483 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7289 (mm-30)
REVERT: B  495 GLU cc_start: 0.7884 (tp30) cc_final: 0.7417 (tp30)
REVERT: B  602 ARG cc_start: 0.8827 (mmm160) cc_final: 0.8542 (mpt-90)
  outliers start: 3
  outliers final: 3
  residues processed: 57
  average time/residue: 1.4812
  time to fit residues: 89.1653
Evaluate side-chains
  57 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 ARG
Chi-restraints excluded: chain B residue  271 SER
Chi-restraints excluded: chain B residue  545 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.100432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.072626 restraints weight = 40843.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 2.42
r_work: 0.2943 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8827  Z= 0.197
  Angle     :  0.528   8.181  12053  Z= 0.271
  Chirality :  0.045   0.154   1333
  Planarity :  0.003   0.040   1519
  Dihedral  :  4.856  30.950   1329
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.32 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.26), residues: 1046
  helix:  3.95 (0.66), residues: 63
  sheet: -0.56 (0.23), residues: 442
  loop : -0.61 (0.27), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 475 
 TYR   0.010   0.001   TYR B 677 
 PHE   0.009   0.001   PHE B 754 
 TRP   0.011   0.001   TRP B 848 
 HIS   0.003   0.001   HIS B 785 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8807)
  covalent geometry    : angle       0.52075 (12004)
  SS BOND              : bond        0.00254 (   11)
  SS BOND              : angle       1.10011 (   22)
  hydrogen bonds       : bond        0.03577 (  293)
  hydrogen bonds       : angle       4.97684 (  834)
  link_NAG-ASN         : bond        0.00270 (    9)
  link_NAG-ASN         : angle       1.73961 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5593.27 seconds
wall clock time: 95 minutes 6.18 seconds (5706.18 seconds total)