Starting phenix.real_space_refine
on Tue Mar  3 22:23:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gjm_51397/03_2026/9gjm_51397.map"
  }
  resolution = 3.9
  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=   0.048
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      88      5.16       5
     C    5392      2.51       5
     N    1455      2.21       5
     O    1768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8703
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 6243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 797, 6243
          Classifications: {'peptide': 797}
          Link IDs: {'PTRANS': 20, 'TRANS': 776}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 2270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2270
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 16, 'TRANS': 258}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "C"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 26
          Unusual residues: {'GAL': 1, 'NDG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.02, per 1000 atoms: 0.23
  Number of scatterers: 8703
  At special positions: 0
  Unit cell: (111.488, 108.992, 110.656, 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      88     16.00
     O    1768      8.00
     N    1455      7.00
     C    5392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=34, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  69 " - pdb=" SG  CYS H  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 104 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 139 " - pdb=" SG  CYS H 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 395 " - pdb=" SG  CYS H 404 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 400 " - pdb=" SG  CYS H 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 412 " - pdb=" SG  CYS H 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 415 " - pdb=" SG  CYS L  75 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 416 " - pdb=" SG  CYS H 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 420 " - pdb=" SG  CYS H 456 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 446 " - pdb=" SG  CYS H 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 450 " - pdb=" SG  CYS H 482 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 471 " - pdb=" SG  CYS H 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 477 " - pdb=" SG  CYS H 515 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 498 " - pdb=" SG  CYS H 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 510 " - pdb=" SG  CYS H 544 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 532 " - pdb=" SG  CYS H 550 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 539 " - pdb=" SG  CYS H 573 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 557 " - pdb=" SG  CYS H 580 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 568 " - pdb=" SG  CYS H 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 586 " - pdb=" SG  CYS H 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 592 " - pdb=" SG  CYS H 630 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 601 " - pdb=" SG  CYS H 613 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 622 " - pdb=" SG  CYS H 639 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 644 " - pdb=" SG  CYS H 658 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 653 " - pdb=" SG  CYS H 697 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 672 " - pdb=" SG  CYS H 702 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 689 " - pdb=" SG  CYS H 718 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 715 " - pdb=" SG  CYS H 746 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 732 " - pdb=" SG  CYS H 756 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 739 " - pdb=" SG  CYS H 775 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 772 " - pdb=" SG  CYS H 798 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 780 " - pdb=" SG  CYS H 811 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  71 " - pdb=" SG  CYS L  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 241 " - pdb=" SG  CYS L 274 " 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
    ALPHA1-2
      " MAN B   4 " - " MAN B   5 "
      " MAN B   5 " - " MAN B   6 "
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   7 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NDG C   1 " - " GAL C   2 "
    NAG-ASN
      " NAG A   1 " - " ASN H 337 "
      " NAG B   1 " - " ASN H 390 "
      " NAG H 901 " - " ASN H 468 "
      " NAG H 902 " - " ASN H 198 "
      " NAG H 903 " - " ASN H 659 "
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 311.3 milliseconds
  

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2032

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 22 sheets defined
      15.3% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'H' and resid 16 through 18
      No H-bonds generated for 'chain 'H' and resid 16 through 18'
    Processing helix  chain 'H' and resid 30 through 34
      removed outlier: 3.609A  pdb=" N   SER H  34 " --> pdb=" O   LEU H  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 30 through 34'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.515A  pdb=" N   ASP H  93 " --> pdb=" O   LYS H  90 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE H  94 " --> pdb=" O   VAL H  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 94'
    Processing helix  chain 'H' and resid 125 through 129
      removed outlier: 3.661A  pdb=" N   ILE H 129 " --> pdb=" O   GLU H 126 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 196
      removed outlier: 3.965A  pdb=" N   ILE H 192 " --> pdb=" O   ASN H 188 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 224 through 235
      removed outlier: 4.325A  pdb=" N   LYS H 229 " --> pdb=" O   SER H 225 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   SER H 230 " --> pdb=" O   THR H 226 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 236 through 240
    Processing helix  chain 'H' and resid 263 through 267
    Processing helix  chain 'H' and resid 268 through 273
      removed outlier: 3.671A  pdb=" N   LEU H 272 " --> pdb=" O   LYS H 268 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 282 through 299
      removed outlier: 3.695A  pdb=" N   ASP H 299 " --> pdb=" O   THR H 295 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 328 through 333
    Processing helix  chain 'H' and resid 350 through 361
      removed outlier: 3.914A  pdb=" N   THR H 354 " --> pdb=" O   ASP H 350 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG H 359 " --> pdb=" O   ARG H 355 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU H 360 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 363 through 365
      No H-bonds generated for 'chain 'H' and resid 363 through 365'
    Processing helix  chain 'H' and resid 375 through 391
      removed outlier: 3.548A  pdb=" N   THR H 379 " --> pdb=" O   GLU H 375 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 560 through 564
    Processing helix  chain 'H' and resid 604 through 608
    Processing helix  chain 'H' and resid 684 through 688
    Processing helix  chain 'H' and resid 767 through 773
    Processing helix  chain 'H' and resid 774 through 776
      No H-bonds generated for 'chain 'H' and resid 774 through 776'
    Processing helix  chain 'L' and resid 92 through 99
    Processing helix  chain 'L' and resid 182 through 187
    Processing helix  chain 'L' and resid 197 through 201
    Processing helix  chain 'L' and resid 254 through 258
      removed outlier: 4.018A  pdb=" N   LYS L 258 " --> pdb=" O   THR L 255 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 278 through 281
    Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108
      removed outlier: 3.583A  pdb=" N   HIS H  63 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   GLY H  36 " --> pdb=" O   ASP H  29 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ASP H  29 " --> pdb=" O   GLY H  36 " (cutoff:3.500A)
      removed outlier: 5.822A  pdb=" N   CYS H 169 " --> pdb=" O   PHE H 181 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   TYR H 152 " --> pdb=" O   CYS H 169 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   MET H 171 " --> pdb=" O   TYR H 150 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   TYR H 150 " --> pdb=" O   MET H 171 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108
      removed outlier: 3.583A  pdb=" N   HIS H  63 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262
      removed outlier: 5.807A  pdb=" N   THR H 214 " --> pdb=" O   LYS H 245 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL H 247 " --> pdb=" O   THR H 214 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   LEU H 216 " --> pdb=" O   VAL H 247 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   LEU H 249 " --> pdb=" O   LEU H 216 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ILE H 218 " --> pdb=" O   LEU H 249 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   TYR H 251 " --> pdb=" O   ILE H 218 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   PHE H 220 " --> pdb=" O   TYR H 251 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   HIS H 215 " --> pdb=" O   ARG H 312 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA H 217 " --> pdb=" O   THR H 314 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 431 through 434
      removed outlier: 4.712A  pdb=" N   CYS H 425 " --> pdb=" O   PRO L 285 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 456
      removed outlier: 6.693A  pdb=" N   SER H 453 " --> pdb=" O   THR H 465 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 478 through 481
    Processing sheet with id=AA7, first strand: chain 'H' and resid 511 through 513
      removed outlier: 6.590A  pdb=" N   SER H 512 " --> pdb=" O   ASP H 525 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 540 through 544
    Processing sheet with id=AA9, first strand: chain 'H' and resid 569 through 572
      removed outlier: 3.505A  pdb=" N   GLU H 581 " --> pdb=" O   LYS H 572 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 601 through 602
      removed outlier: 4.253A  pdb=" N   LYS H 602 " --> pdb=" O   GLN H 612 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN H 612 " --> pdb=" O   LYS H 602 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'H' and resid 628 through 630
    Processing sheet with id=AB3, first strand: chain 'H' and resid 650 through 651
    Processing sheet with id=AB4, first strand: chain 'H' and resid 693 through 698
    Processing sheet with id=AB5, first strand: chain 'H' and resid 717 through 718
    Processing sheet with id=AB6, first strand: chain 'H' and resid 745 through 749
    Processing sheet with id=AB7, first strand: chain 'H' and resid 788 through 791
    Processing sheet with id=AB8, first strand: chain 'H' and resid 809 through 812
    Processing sheet with id=AB9, first strand: chain 'L' and resid 41 through 42
      removed outlier: 6.327A  pdb=" N   PHE L  41 " --> pdb=" O   ASN L 261 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'L' and resid 103 through 106
      removed outlier: 4.836A  pdb=" N   LEU L 240 " --> pdb=" O   LEU L 232 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   PHE L 230 " --> pdb=" O   TYR L 242 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'L' and resid 124 through 125
      removed outlier: 4.665A  pdb=" N   GLN L 124 " --> pdb=" O   ILE L 172 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'L' and resid 140 through 143
    Processing sheet with id=AC4, first strand: chain 'L' and resid 208 through 212

    250 hydrogen bonds defined for protein.
    633 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: 1.46

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2797
        1.34 -     1.46: 2075
        1.46 -     1.58: 3897
        1.58 -     1.70: 0
        1.70 -     1.82: 106
  Bond restraints: 8875
  Sorted by residual:
  bond pdb=" N   ASN H 234 "
       pdb=" CA  ASN H 234 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.32e-02 5.74e+03 6.49e+00
  bond pdb=" N   LEU H 235 "
       pdb=" CA  LEU H 235 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.35e-02 5.49e+03 5.56e+00
  bond pdb=" N   SER H 236 "
       pdb=" CA  SER H 236 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.30e-02 5.92e+03 4.33e+00
  bond pdb=" C   ASN H 234 "
       pdb=" O   ASN H 234 "
    ideal  model  delta    sigma   weight residual
    1.236  1.259 -0.023 1.28e-02 6.10e+03 3.27e+00
  bond pdb=" CB  LYS H 290 "
       pdb=" CG  LYS H 290 "
    ideal  model  delta    sigma   weight residual
    1.520  1.468  0.052 3.00e-02 1.11e+03 3.02e+00
  ... (remaining 8870 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 11682
        1.83 -     3.67: 270
        3.67 -     5.50: 38
        5.50 -     7.33: 10
        7.33 -     9.17: 4
  Bond angle restraints: 12004
  Sorted by residual:
  angle pdb=" CA  MET H 407 "
        pdb=" C   MET H 407 "
        pdb=" N   ASN H 408 "
      ideal   model   delta    sigma   weight residual
     117.92  110.52    7.40 1.35e+00 5.49e-01 3.00e+01
  angle pdb=" C   ALA H 406 "
        pdb=" N   MET H 407 "
        pdb=" CA  MET H 407 "
      ideal   model   delta    sigma   weight residual
     122.66  115.42    7.24 1.63e+00 3.76e-01 1.97e+01
  angle pdb=" CA  GLN H 266 "
        pdb=" CB  GLN H 266 "
        pdb=" CG  GLN H 266 "
      ideal   model   delta    sigma   weight residual
     114.10  121.86   -7.76 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" CA  GLU H 547 "
        pdb=" CB  GLU H 547 "
        pdb=" CG  GLU H 547 "
      ideal   model   delta    sigma   weight residual
     114.10  120.58   -6.48 2.00e+00 2.50e-01 1.05e+01
  angle pdb=" C   GLN H 194 "
        pdb=" CA  GLN H 194 "
        pdb=" CB  GLN H 194 "
      ideal   model   delta    sigma   weight residual
     109.24  114.39   -5.15 1.75e+00 3.27e-01 8.67e+00
  ... (remaining 11999 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.26: 4868
       19.26 -    38.53: 622
       38.53 -    57.79: 133
       57.79 -    77.05: 34
       77.05 -    96.32: 14
  Dihedral angle restraints: 5671
    sinusoidal: 2502
      harmonic: 3169
  Sorted by residual:
  dihedral pdb=" CB  CYS H 446 "
           pdb=" SG  CYS H 446 "
           pdb=" SG  CYS H 462 "
           pdb=" CB  CYS H 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  172.53  -79.53     1      1.00e+01 1.00e-02 7.86e+01
  dihedral pdb=" CB  CYS H 586 "
           pdb=" SG  CYS H 586 "
           pdb=" SG  CYS H 611 "
           pdb=" CB  CYS H 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   31.92   61.08     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" CB  CYS H 539 "
           pdb=" SG  CYS H 539 "
           pdb=" SG  CYS H 573 "
           pdb=" CB  CYS H 573 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.31  -49.69     1      1.00e+01 1.00e-02 3.39e+01
  ... (remaining 5668 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1075
       0.052 -    0.103: 223
       0.103 -    0.155: 46
       0.155 -    0.206: 4
       0.206 -    0.258: 1
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN H 337 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE H 338 "
            pdb=" N   ILE H 338 "
            pdb=" C   ILE H 338 "
            pdb=" CB  ILE H 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN H 390 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.62e-01
  ... (remaining 1346 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN H 337 "   -0.001 2.00e-02 2.50e+03   3.24e-02 1.31e+01
        pdb=" CG  ASN H 337 "   -0.029 2.00e-02 2.50e+03
        pdb=" OD1 ASN H 337 "    0.037 2.00e-02 2.50e+03
        pdb=" ND2 ASN H 337 "   -0.042 2.00e-02 2.50e+03
        pdb=" C1  NAG A   1 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN H 699 "    0.013 2.00e-02 2.50e+03   2.59e-02 6.72e+00
        pdb=" C   ASN H 699 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   ASN H 699 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLY H 700 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP L 223 "    0.038 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO L 224 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO L 224 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO L 224 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 260
        2.68 -     3.23: 8649
        3.23 -     3.79: 13599
        3.79 -     4.34: 18053
        4.34 -     4.90: 29094
  Nonbonded interactions: 69655
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L 262 "
            pdb=" O   SER L 264 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD1 ASP L 106 "
            pdb=" N   MET L 107 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   CYS H 672 "
            pdb=" OG1 THR H 675 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OG1 THR H 263 "
            pdb=" OD1 ASP H 265 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLN H 266 "
            pdb=" NE2 GLN H 266 "
     model   vdw
     2.243 3.120
  ... (remaining 69650 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.320
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6846
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8923  Z= 0.155
  Angle     :  0.716  11.929  12114  Z= 0.386
  Chirality :  0.045   0.258   1349
  Planarity :  0.004   0.057   1532
  Dihedral  : 17.466  96.317   3537
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 26.40 %
    Favored  : 73.29 %
  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: 1066
  helix: -1.54 (0.46), residues: 110
  sheet:  0.09 (0.32), residues: 263
  loop : -0.26 (0.24), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 355 
 TYR   0.023   0.002   TYR H 195 
 PHE   0.012   0.001   PHE L  91 
 TRP   0.011   0.002   TRP H  66 
 HIS   0.007   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8875)
  covalent geometry    : angle       0.68601 (12004)
  SS BOND              : bond        0.00314 (   34)
  SS BOND              : angle       1.51979 (   68)
  hydrogen bonds       : bond        0.17655 (  225)
  hydrogen bonds       : angle       7.46192 (  633)
  link_ALPHA1-2        : bond        0.00175 (    2)
  link_ALPHA1-2        : angle       1.56856 (    6)
  link_ALPHA1-3        : bond        0.00252 (    1)
  link_ALPHA1-3        : angle       1.55568 (    3)
  link_ALPHA1-6        : bond        0.00279 (    1)
  link_ALPHA1-6        : angle       1.50014 (    3)
  link_BETA1-4         : bond        0.00615 (    5)
  link_BETA1-4         : angle       1.98653 (   15)
  link_NAG-ASN         : bond        0.00745 (    5)
  link_NAG-ASN         : angle       4.52989 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  293 LEU cc_start: 0.8965 (mm) cc_final: 0.8722 (mm)
  outliers start: 3
  outliers final: 2
  residues processed: 101
  average time/residue: 0.0876
  time to fit residues: 12.8626
Evaluate side-chains
  97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  772 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** H  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  51 GLN
L  56 ASN
L 243 GLN
L 281 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.168732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.136016 restraints weight = 19080.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.137618 restraints weight = 16716.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.138710 restraints weight = 13295.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.139663 restraints weight = 8536.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.140354 restraints weight = 7598.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.0780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8923  Z= 0.113
  Angle     :  0.608   9.029  12114  Z= 0.310
  Chirality :  0.044   0.208   1349
  Planarity :  0.004   0.053   1532
  Dihedral  :  9.801  80.135   1486
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.88 %
    Favored  : 74.43 %
  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: -0.24 (0.26), residues: 1066
  helix: -0.57 (0.51), residues: 105
  sheet:  0.31 (0.32), residues: 256
  loop : -0.22 (0.24), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 553 
 TYR   0.010   0.001   TYR H 195 
 PHE   0.012   0.001   PHE L 287 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8875)
  covalent geometry    : angle       0.58200 (12004)
  SS BOND              : bond        0.00255 (   34)
  SS BOND              : angle       1.00882 (   68)
  hydrogen bonds       : bond        0.03890 (  225)
  hydrogen bonds       : angle       6.10001 (  633)
  link_ALPHA1-2        : bond        0.00313 (    2)
  link_ALPHA1-2        : angle       1.62843 (    6)
  link_ALPHA1-3        : bond        0.00967 (    1)
  link_ALPHA1-3        : angle       1.45290 (    3)
  link_ALPHA1-6        : bond        0.00445 (    1)
  link_ALPHA1-6        : angle       1.49381 (    3)
  link_BETA1-4         : bond        0.00575 (    5)
  link_BETA1-4         : angle       2.24799 (   15)
  link_NAG-ASN         : bond        0.00720 (    5)
  link_NAG-ASN         : angle       4.03357 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  129 ILE cc_start: 0.8008 (mm) cc_final: 0.7778 (mm)
REVERT: H  345 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8137 (mp)
REVERT: H  414 MET cc_start: 0.8208 (mmm) cc_final: 0.7925 (mmm)
REVERT: H  561 SER cc_start: 0.8637 (m) cc_final: 0.8067 (p)
REVERT: L   51 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7583 (pp30)
  outliers start: 26
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0930
  time to fit residues: 16.5554
Evaluate side-chains
  110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 HIS
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue  150 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 77 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0770
   chunk 13 optimal weight:    0.7980
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    0.4980
   chunk 70 optimal weight:   50.0000
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.2540

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

Flipped N/Q/H residues before XYZ refinement:
H  48 HIS
H 266 GLN
L  51 GLN
L  56 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.166766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.132592 restraints weight = 19487.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.131445 restraints weight = 16329.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.133335 restraints weight = 12834.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.134402 restraints weight = 8514.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.134892 restraints weight = 8088.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.089   8923  Z= 0.137
  Angle     :  0.638  15.454  12114  Z= 0.322
  Chirality :  0.045   0.249   1349
  Planarity :  0.004   0.050   1532
  Dihedral  :  8.664  67.046   1483
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 21.95 %
    Favored  : 74.64 %
  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: -0.24 (0.26), residues: 1066
  helix: -0.48 (0.50), residues: 112
  sheet:  0.40 (0.33), residues: 247
  loop : -0.27 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  76 
 TYR   0.027   0.001   TYR L  26 
 PHE   0.014   0.001   PHE L  91 
 TRP   0.011   0.001   TRP H 435 
 HIS   0.003   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 8875)
  covalent geometry    : angle       0.60643 (12004)
  SS BOND              : bond        0.00276 (   34)
  SS BOND              : angle       1.62680 (   68)
  hydrogen bonds       : bond        0.03532 (  225)
  hydrogen bonds       : angle       5.83170 (  633)
  link_ALPHA1-2        : bond        0.00226 (    2)
  link_ALPHA1-2        : angle       1.74013 (    6)
  link_ALPHA1-3        : bond        0.00836 (    1)
  link_ALPHA1-3        : angle       1.85459 (    3)
  link_ALPHA1-6        : bond        0.00365 (    1)
  link_ALPHA1-6        : angle       1.49741 (    3)
  link_BETA1-4         : bond        0.00618 (    5)
  link_BETA1-4         : angle       2.27676 (   15)
  link_NAG-ASN         : bond        0.00681 (    5)
  link_NAG-ASN         : angle       3.89271 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 TYR cc_start: 0.7721 (t80) cc_final: 0.7493 (t80)
REVERT: H  129 ILE cc_start: 0.8032 (mm) cc_final: 0.7789 (mm)
REVERT: H  414 MET cc_start: 0.8274 (mmm) cc_final: 0.7971 (tpp)
REVERT: L   51 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7371 (pp30)
REVERT: L  106 ASP cc_start: 0.6867 (t0) cc_final: 0.6635 (t0)
REVERT: L  194 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7692 (m-70)
  outliers start: 33
  outliers final: 18
  residues processed: 133
  average time/residue: 0.0834
  time to fit residues: 15.9967
Evaluate side-chains
  114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 48 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
H  48 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.162690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.129885 restraints weight = 19314.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.130251 restraints weight = 17141.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.131652 restraints weight = 13364.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.133316 restraints weight = 8651.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.133658 restraints weight = 7484.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6984
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   8923  Z= 0.188
  Angle     :  0.651  10.370  12114  Z= 0.332
  Chirality :  0.046   0.238   1349
  Planarity :  0.004   0.046   1532
  Dihedral  :  8.044  56.873   1483
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 22.26 %
    Favored  : 74.12 %
  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: -0.39 (0.25), residues: 1066
  helix: -0.39 (0.51), residues: 112
  sheet:  0.17 (0.33), residues: 250
  loop : -0.35 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  76 
 TYR   0.017   0.002   TYR H 569 
 PHE   0.015   0.002   PHE L  91 
 TRP   0.012   0.002   TRP H 435 
 HIS   0.006   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8875)
  covalent geometry    : angle       0.61813 (12004)
  SS BOND              : bond        0.00357 (   34)
  SS BOND              : angle       1.61605 (   68)
  hydrogen bonds       : bond        0.03451 (  225)
  hydrogen bonds       : angle       5.89202 (  633)
  link_ALPHA1-2        : bond        0.00198 (    2)
  link_ALPHA1-2        : angle       2.08994 (    6)
  link_ALPHA1-3        : bond        0.01013 (    1)
  link_ALPHA1-3        : angle       2.53320 (    3)
  link_ALPHA1-6        : bond        0.00449 (    1)
  link_ALPHA1-6        : angle       1.58345 (    3)
  link_BETA1-4         : bond        0.00735 (    5)
  link_BETA1-4         : angle       2.43012 (   15)
  link_NAG-ASN         : bond        0.00705 (    5)
  link_NAG-ASN         : angle       3.83564 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 92
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 TYR cc_start: 0.7859 (t80) cc_final: 0.7629 (t80)
REVERT: H  129 ILE cc_start: 0.8015 (mm) cc_final: 0.7725 (mm)
REVERT: L  194 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7833 (m-70)
  outliers start: 35
  outliers final: 27
  residues processed: 121
  average time/residue: 0.0884
  time to fit residues: 15.5063
Evaluate side-chains
  114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 86
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  451 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain H residue  810 VAL
Chi-restraints excluded: chain L residue   75 CYS
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  171 ILE
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  221 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 98 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 59 optimal weight:   10.0000
   chunk 68 optimal weight:    7.9990
   chunk 102 optimal weight:    8.9990
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
H  48 HIS
H 328 ASN
** H 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 125 ASN
** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 176 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.160470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.128348 restraints weight = 19225.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.128787 restraints weight = 17152.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.130002 restraints weight = 14525.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.130807 restraints weight = 9291.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.132056 restraints weight = 8103.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8923  Z= 0.201
  Angle     :  0.668  10.031  12114  Z= 0.340
  Chirality :  0.047   0.265   1349
  Planarity :  0.004   0.044   1532
  Dihedral  :  7.582  52.022   1483
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 22.36 %
    Favored  : 73.08 %
  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 (0.25), residues: 1066
  helix: -0.40 (0.51), residues: 118
  sheet:  0.19 (0.33), residues: 248
  loop : -0.40 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG H 355 
 TYR   0.016   0.002   TYR H 569 
 PHE   0.016   0.002   PHE L 140 
 TRP   0.012   0.002   TRP H 435 
 HIS   0.008   0.002   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 8875)
  covalent geometry    : angle       0.63900 (12004)
  SS BOND              : bond        0.00473 (   34)
  SS BOND              : angle       1.30141 (   68)
  hydrogen bonds       : bond        0.03425 (  225)
  hydrogen bonds       : angle       5.98171 (  633)
  link_ALPHA1-2        : bond        0.00504 (    2)
  link_ALPHA1-2        : angle       2.18486 (    6)
  link_ALPHA1-3        : bond        0.00584 (    1)
  link_ALPHA1-3        : angle       2.44755 (    3)
  link_ALPHA1-6        : bond        0.00081 (    1)
  link_ALPHA1-6        : angle       1.32148 (    3)
  link_BETA1-4         : bond        0.00767 (    5)
  link_BETA1-4         : angle       2.70804 (   15)
  link_NAG-ASN         : bond        0.00702 (    5)
  link_NAG-ASN         : angle       3.85279 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 88
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  293 LEU cc_start: 0.8945 (mm) cc_final: 0.8702 (mm)
  outliers start: 44
  outliers final: 31
  residues processed: 121
  average time/residue: 0.0810
  time to fit residues: 14.6748
Evaluate side-chains
  110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  169 CYS
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  451 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain H residue  729 HIS
Chi-restraints excluded: chain H residue  810 VAL
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  171 ILE
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  221 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 29 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 103 optimal weight:   30.0000
   chunk 59 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0470
   overall best weight:    1.8086

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

Flipped N/Q/H residues before XYZ refinement:
H  48 HIS
H  49 GLN
L  56 ASN
** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 176 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.161336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.129475 restraints weight = 19201.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.129965 restraints weight = 17376.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.131098 restraints weight = 15014.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.132336 restraints weight = 9429.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.133038 restraints weight = 8076.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8923  Z= 0.152
  Angle     :  0.623   8.956  12114  Z= 0.318
  Chirality :  0.045   0.219   1349
  Planarity :  0.004   0.046   1532
  Dihedral  :  7.300  54.555   1483
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 22.88 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.25), residues: 1066
  helix: -0.48 (0.49), residues: 124
  sheet:  0.26 (0.33), residues: 248
  loop : -0.44 (0.23), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 553 
 TYR   0.016   0.001   TYR H  46 
 PHE   0.016   0.002   PHE L  91 
 TRP   0.012   0.001   TRP H  66 
 HIS   0.004   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8875)
  covalent geometry    : angle       0.59622 (12004)
  SS BOND              : bond        0.00399 (   34)
  SS BOND              : angle       1.29329 (   68)
  hydrogen bonds       : bond        0.03109 (  225)
  hydrogen bonds       : angle       5.83701 (  633)
  link_ALPHA1-2        : bond        0.00453 (    2)
  link_ALPHA1-2        : angle       2.09386 (    6)
  link_ALPHA1-3        : bond        0.00883 (    1)
  link_ALPHA1-3        : angle       1.96703 (    3)
  link_ALPHA1-6        : bond        0.00332 (    1)
  link_ALPHA1-6        : angle       1.38828 (    3)
  link_BETA1-4         : bond        0.00706 (    5)
  link_BETA1-4         : angle       2.57421 (   15)
  link_NAG-ASN         : bond        0.00804 (    5)
  link_NAG-ASN         : angle       3.45268 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 90
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  293 LEU cc_start: 0.8935 (mm) cc_final: 0.8694 (mm)
REVERT: H  345 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8045 (mp)
REVERT: L  188 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7332 (mm-40)
  outliers start: 43
  outliers final: 36
  residues processed: 125
  average time/residue: 0.0786
  time to fit residues: 14.7139
Evaluate side-chains
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   49 GLN
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  169 CYS
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  315 MET
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  451 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  515 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain H residue  810 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  149 THR
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  160 ILE
Chi-restraints excluded: chain L residue  175 LYS
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain L residue  221 LEU
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 70 optimal weight:   30.0000
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 76 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 102 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
H  48 HIS
H 699 ASN
** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 176 ASN
L 268 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.157237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.115535 restraints weight = 19495.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.115889 restraints weight = 11061.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.117152 restraints weight = 9001.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.116938 restraints weight = 7344.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.117335 restraints weight = 7658.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   8923  Z= 0.268
  Angle     :  0.706   8.947  12114  Z= 0.364
  Chirality :  0.047   0.228   1349
  Planarity :  0.005   0.041   1532
  Dihedral  :  7.624  59.499   1483
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.98 %
    Favored  : 72.26 %
  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: -0.64 (0.25), residues: 1066
  helix: -0.61 (0.48), residues: 123
  sheet:  0.19 (0.33), residues: 235
  loop : -0.59 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 553 
 TYR   0.023   0.002   TYR H 569 
 PHE   0.022   0.002   PHE L 230 
 TRP   0.015   0.002   TRP H 435 
 HIS   0.006   0.002   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 8875)
  covalent geometry    : angle       0.67607 (12004)
  SS BOND              : bond        0.00503 (   34)
  SS BOND              : angle       1.45504 (   68)
  hydrogen bonds       : bond        0.03569 (  225)
  hydrogen bonds       : angle       6.12032 (  633)
  link_ALPHA1-2        : bond        0.00941 (    2)
  link_ALPHA1-2        : angle       2.44400 (    6)
  link_ALPHA1-3        : bond        0.00393 (    1)
  link_ALPHA1-3        : angle       3.15310 (    3)
  link_ALPHA1-6        : bond        0.00254 (    1)
  link_ALPHA1-6        : angle       1.57373 (    3)
  link_BETA1-4         : bond        0.00785 (    5)
  link_BETA1-4         : angle       2.86244 (   15)
  link_NAG-ASN         : bond        0.00958 (    5)
  link_NAG-ASN         : angle       3.77580 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 81
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  170 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7941 (ttm-80)
REVERT: H  293 LEU cc_start: 0.9247 (mm) cc_final: 0.8989 (mm)
REVERT: H  684 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8289 (tptt)
REVERT: H  688 MET cc_start: 0.8691 (pmm) cc_final: 0.8200 (pmm)
REVERT: L  188 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6600 (mm-40)
  outliers start: 46
  outliers final: 37
  residues processed: 116
  average time/residue: 0.0793
  time to fit residues: 13.6316
Evaluate side-chains
  115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  169 CYS
Chi-restraints excluded: chain H residue  170 ARG
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  315 MET
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  338 ILE
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  515 CYS
Chi-restraints excluded: chain H residue  543 VAL
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain H residue  729 HIS
Chi-restraints excluded: chain H residue  810 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  160 ILE
Chi-restraints excluded: chain L residue  171 ILE
Chi-restraints excluded: chain L residue  175 LYS
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain L residue  221 LEU
Chi-restraints excluded: chain L residue  260 LEU
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 60 optimal weight:   30.0000
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
H 291 ASN
L  56 ASN
** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.160223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.128376 restraints weight = 19028.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.130272 restraints weight = 17518.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.131320 restraints weight = 13181.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.132808 restraints weight = 8842.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.133144 restraints weight = 7764.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8923  Z= 0.140
  Angle     :  0.632   8.945  12114  Z= 0.323
  Chirality :  0.045   0.217   1349
  Planarity :  0.004   0.046   1532
  Dihedral  :  7.085  51.696   1483
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.19 %
    Favored  : 72.26 %
  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: -0.49 (0.25), residues: 1066
  helix: -0.62 (0.48), residues: 124
  sheet:  0.25 (0.34), residues: 227
  loop : -0.43 (0.23), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  76 
 TYR   0.016   0.001   TYR H  46 
 PHE   0.021   0.002   PHE L  91 
 TRP   0.013   0.002   TRP H  66 
 HIS   0.003   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8875)
  covalent geometry    : angle       0.60640 (12004)
  SS BOND              : bond        0.00372 (   34)
  SS BOND              : angle       1.15958 (   68)
  hydrogen bonds       : bond        0.03095 (  225)
  hydrogen bonds       : angle       5.91848 (  633)
  link_ALPHA1-2        : bond        0.00426 (    2)
  link_ALPHA1-2        : angle       2.31998 (    6)
  link_ALPHA1-3        : bond        0.00975 (    1)
  link_ALPHA1-3        : angle       1.70604 (    3)
  link_ALPHA1-6        : bond        0.00386 (    1)
  link_ALPHA1-6        : angle       1.41812 (    3)
  link_BETA1-4         : bond        0.00742 (    5)
  link_BETA1-4         : angle       2.63381 (   15)
  link_NAG-ASN         : bond        0.00745 (    5)
  link_NAG-ASN         : angle       3.41561 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 86
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  170 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7630 (ttm-80)
REVERT: H  293 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8743 (mm)
REVERT: H  345 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8073 (mp)
REVERT: H  688 MET cc_start: 0.8662 (pmm) cc_final: 0.8061 (pmm)
REVERT: L   56 ASN cc_start: 0.7242 (m-40) cc_final: 0.7017 (m110)
REVERT: L  188 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7245 (mm-40)
  outliers start: 44
  outliers final: 34
  residues processed: 122
  average time/residue: 0.0766
  time to fit residues: 14.0180
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 79
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  169 CYS
Chi-restraints excluded: chain H residue  170 ARG
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  293 LEU
Chi-restraints excluded: chain H residue  315 MET
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  338 ILE
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  345 LEU
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  451 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  515 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain H residue  810 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  160 ILE
Chi-restraints excluded: chain L residue  175 LYS
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain L residue  221 LEU
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 87 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 104 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
L 243 GLN
L 281 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.155384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.113815 restraints weight = 19267.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.113928 restraints weight = 11316.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114982 restraints weight = 9354.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.114819 restraints weight = 7545.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.115063 restraints weight = 7820.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   8923  Z= 0.293
  Angle     :  0.754   8.196  12114  Z= 0.389
  Chirality :  0.048   0.233   1349
  Planarity :  0.005   0.045   1532
  Dihedral  :  7.425  51.473   1483
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.29 %
    Favored  : 72.15 %
  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: -0.86 (0.25), residues: 1066
  helix: -0.84 (0.47), residues: 123
  sheet: -0.12 (0.33), residues: 245
  loop : -0.67 (0.23), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  76 
 TYR   0.029   0.002   TYR L 231 
 PHE   0.030   0.003   PHE L 230 
 TRP   0.018   0.002   TRP H 435 
 HIS   0.007   0.002   HIS L 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 8875)
  covalent geometry    : angle       0.72565 (12004)
  SS BOND              : bond        0.00530 (   34)
  SS BOND              : angle       1.43811 (   68)
  hydrogen bonds       : bond        0.03729 (  225)
  hydrogen bonds       : angle       6.24929 (  633)
  link_ALPHA1-2        : bond        0.01115 (    2)
  link_ALPHA1-2        : angle       2.72105 (    6)
  link_ALPHA1-3        : bond        0.00312 (    1)
  link_ALPHA1-3        : angle       3.47194 (    3)
  link_ALPHA1-6        : bond        0.00415 (    1)
  link_ALPHA1-6        : angle       1.76401 (    3)
  link_BETA1-4         : bond        0.00705 (    5)
  link_BETA1-4         : angle       2.99033 (   15)
  link_NAG-ASN         : bond        0.01003 (    5)
  link_NAG-ASN         : angle       3.66168 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 80
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   94 ILE cc_start: 0.8505 (pt) cc_final: 0.8301 (mm)
REVERT: H  167 ASP cc_start: 0.8319 (t70) cc_final: 0.7678 (t70)
REVERT: H  170 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7897 (ttm-80)
REVERT: H  192 ILE cc_start: 0.9054 (pt) cc_final: 0.8826 (tt)
REVERT: H  293 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9051 (mm)
REVERT: H  684 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8354 (tptt)
REVERT: H  688 MET cc_start: 0.8660 (pmm) cc_final: 0.8220 (pmm)
REVERT: L  147 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7005 (ttm)
REVERT: L  188 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6613 (mm-40)
REVERT: L  194 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.8101 (m-70)
  outliers start: 44
  outliers final: 29
  residues processed: 116
  average time/residue: 0.0800
  time to fit residues: 13.5648
Evaluate side-chains
  109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 75
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  170 ARG
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  293 LEU
Chi-restraints excluded: chain H residue  315 MET
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  515 CYS
Chi-restraints excluded: chain H residue  543 VAL
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  147 MET
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  160 ILE
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain L residue  221 LEU
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 0 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 41 optimal weight:    9.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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 = 0.4437 r_free = 0.4437 target = 0.159351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.127379 restraints weight = 19071.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.127963 restraints weight = 17536.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.128911 restraints weight = 13225.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.131757 restraints weight = 9155.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.131769 restraints weight = 6510.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8923  Z= 0.136
  Angle     :  0.651   8.861  12114  Z= 0.331
  Chirality :  0.045   0.217   1349
  Planarity :  0.004   0.044   1532
  Dihedral  :  6.771  50.737   1483
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.02 %
    Favored  : 72.36 %
  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: -0.55 (0.26), residues: 1066
  helix: -0.40 (0.51), residues: 111
  sheet: -0.10 (0.34), residues: 230
  loop : -0.41 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  76 
 TYR   0.028   0.001   TYR L 231 
 PHE   0.022   0.001   PHE L  91 
 TRP   0.017   0.002   TRP L 223 
 HIS   0.004   0.001   HIS L 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8875)
  covalent geometry    : angle       0.62276 (12004)
  SS BOND              : bond        0.00359 (   34)
  SS BOND              : angle       1.44282 (   68)
  hydrogen bonds       : bond        0.03089 (  225)
  hydrogen bonds       : angle       5.91794 (  633)
  link_ALPHA1-2        : bond        0.00422 (    2)
  link_ALPHA1-2        : angle       2.50050 (    6)
  link_ALPHA1-3        : bond        0.01018 (    1)
  link_ALPHA1-3        : angle       1.54130 (    3)
  link_ALPHA1-6        : bond        0.00480 (    1)
  link_ALPHA1-6        : angle       1.28062 (    3)
  link_BETA1-4         : bond        0.00760 (    5)
  link_BETA1-4         : angle       2.66497 (   15)
  link_NAG-ASN         : bond        0.00773 (    5)
  link_NAG-ASN         : angle       3.42455 (   15)

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

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

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2132 Ramachandran restraints generated.
    1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 86
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  167 ASP cc_start: 0.8547 (t70) cc_final: 0.7925 (t70)
REVERT: H  240 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8248 (tp-100)
REVERT: H  293 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8789 (mm)
REVERT: H  407 MET cc_start: 0.7288 (ppp) cc_final: 0.6873 (ppp)
REVERT: H  684 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8352 (tptt)
REVERT: H  688 MET cc_start: 0.8657 (pmm) cc_final: 0.8017 (pmm)
REVERT: L  147 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.5954 (ttm)
REVERT: L  188 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7203 (mm-40)
REVERT: L  194 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.8036 (m-70)
  outliers start: 35
  outliers final: 27
  residues processed: 116
  average time/residue: 0.0844
  time to fit residues: 14.3267
Evaluate side-chains
  114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   24 ASP
Chi-restraints excluded: chain H residue   67 THR
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  107 GLU
Chi-restraints excluded: chain H residue  151 VAL
Chi-restraints excluded: chain H residue  194 GLN
Chi-restraints excluded: chain H residue  240 GLN
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  287 ASN
Chi-restraints excluded: chain H residue  293 LEU
Chi-restraints excluded: chain H residue  315 MET
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  392 THR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  451 VAL
Chi-restraints excluded: chain H residue  515 CYS
Chi-restraints excluded: chain H residue  573 CYS
Chi-restraints excluded: chain H residue  604 ASP
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  704 VAL
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue  126 ILE
Chi-restraints excluded: chain L residue  147 MET
Chi-restraints excluded: chain L residue  150 SER
Chi-restraints excluded: chain L residue  160 ILE
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  198 THR
Chi-restraints excluded: chain L residue  221 LEU
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 71 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 84 optimal weight:    0.3980
   chunk 85 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
L  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.157633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.125852 restraints weight = 19010.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.126045 restraints weight = 17691.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.126797 restraints weight = 14676.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.129579 restraints weight = 9829.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.129773 restraints weight = 6894.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8923  Z= 0.187
  Angle     :  0.678   8.526  12114  Z= 0.347
  Chirality :  0.046   0.222   1349
  Planarity :  0.004   0.043   1532
  Dihedral  :  6.730  50.981   1483
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.71 %
    Favored  : 72.15 %
  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: -0.67 (0.25), residues: 1066
  helix: -0.63 (0.49), residues: 117
  sheet: -0.08 (0.34), residues: 230
  loop : -0.50 (0.23), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  76 
 TYR   0.028   0.002   TYR L 231 
 PHE   0.014   0.002   PHE L 230 
 TRP   0.011   0.002   TRP L 223 
 HIS   0.005   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 8875)
  covalent geometry    : angle       0.65184 (12004)
  SS BOND              : bond        0.00398 (   34)
  SS BOND              : angle       1.31489 (   68)
  hydrogen bonds       : bond        0.03319 (  225)
  hydrogen bonds       : angle       5.95213 (  633)
  link_ALPHA1-2        : bond        0.00572 (    2)
  link_ALPHA1-2        : angle       2.35660 (    6)
  link_ALPHA1-3        : bond        0.00766 (    1)
  link_ALPHA1-3        : angle       2.32191 (    3)
  link_ALPHA1-6        : bond        0.00064 (    1)
  link_ALPHA1-6        : angle       1.49315 (    3)
  link_BETA1-4         : bond        0.00726 (    5)
  link_BETA1-4         : angle       2.70582 (   15)
  link_NAG-ASN         : bond        0.00848 (    5)
  link_NAG-ASN         : angle       3.44372 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1455.43 seconds
wall clock time: 26 minutes 4.07 seconds (1564.07 seconds total)