Starting phenix.real_space_refine
on Tue Mar  3 22:17:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gjj_51394/03_2026/9gjj_51394.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gjj_51394/03_2026/9gjj_51394.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/9gjj_51394/03_2026/9gjj_51394.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gjj_51394/03_2026/9gjj_51394.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gjj_51394/03_2026/9gjj_51394.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gjj_51394/03_2026/9gjj_51394.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=   0.003 sd=   0.076
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    5384      2.51       5
     N    1454      2.21       5
     O    1763      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8689
  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: "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
    Chain: "L"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'GAL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.06, per 1000 atoms: 0.24
  Number of scatterers: 8689
  At special positions: 0
  Unit cell: (110.656, 108.992, 113.152, 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    1763      8.00
     N    1454      7.00
     C    5384      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=2.03
    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=2.02
    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=2.03
    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 "
    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: 0.59
  Conformation dependent library (CDL) restraints added in 258.8 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:
      23 helices and 24 sheets defined
      15.0% alpha, 28.5% 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 90 through 94
      removed outlier: 3.982A  pdb=" N   ILE H  94 " --> pdb=" O   VAL H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 125 through 129
      removed outlier: 3.592A  pdb=" N   ILE H 129 " --> pdb=" O   GLU H 126 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 188 through 196
      removed outlier: 3.721A  pdb=" N   ILE H 192 " --> pdb=" O   ASN H 188 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 224 through 235
      removed outlier: 4.320A  pdb=" N   LYS H 229 " --> pdb=" O   SER H 225 " (cutoff:3.500A)
      removed outlier: 5.683A  pdb=" N   SER H 230 " --> pdb=" O   THR H 226 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 236 through 241
    Processing helix  chain 'H' and resid 263 through 267
    Processing helix  chain 'H' and resid 268 through 273
    Processing helix  chain 'H' and resid 282 through 299
      removed outlier: 3.547A  pdb=" N   ASP H 299 " --> pdb=" O   THR H 295 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 328 through 333
      removed outlier: 3.537A  pdb=" N   GLU H 332 " --> pdb=" O   ASN H 328 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 350 through 361
      removed outlier: 3.851A  pdb=" N   THR H 354 " --> pdb=" O   ASP H 350 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ARG H 359 " --> pdb=" O   ARG H 355 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU H 360 " --> pdb=" O   SER H 356 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL H 361 " --> pdb=" O   ALA H 357 " (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 372 through 374
      No H-bonds generated for 'chain 'H' and resid 372 through 374'
    Processing helix  chain 'H' and resid 375 through 391
    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 689
      removed outlier: 3.725A  pdb=" N   MET H 688 " --> pdb=" O   LYS H 684 " (cutoff:3.500A)
    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 106 through 108
      removed outlier: 3.772A  pdb=" N   HIS H  63 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLY H  36 " --> pdb=" O   ASP H  29 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASP H  29 " --> pdb=" O   GLY H  36 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ARG H 177 " --> pdb=" O   PHE H 173 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   CYS H 169 " --> pdb=" O   PHE H 181 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   VAL H 168 " --> pdb=" O   LEU H 153 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   LEU H 153 " --> pdb=" O   VAL H 168 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ARG H 170 " --> pdb=" O   VAL H 151 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   VAL H 151 " --> pdb=" O   ARG H 170 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASP H 172 " --> pdb=" O   ALA H 149 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 106 through 108
      removed outlier: 3.772A  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: 7.437A  pdb=" N   THR H 214 " --> pdb=" O   GLY H 246 " (cutoff:3.500A)
      removed outlier: 8.693A  pdb=" N   THR H 248 " --> pdb=" O   THR H 214 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   LEU H 216 " --> pdb=" O   THR H 248 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   TYR H 250 " --> pdb=" O   LEU H 216 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   ILE H 218 " --> pdb=" O   TYR H 250 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   LEU H 252 " --> pdb=" O   ILE H 218 " (cutoff:3.500A)
      removed outlier: 8.936A  pdb=" N   PHE H 220 " --> pdb=" O   LEU H 252 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   HIS H 215 " --> pdb=" O   ARG H 312 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   GLY H 313 " --> pdb=" O   SER H 339 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   HIS H 341 " --> pdb=" O   GLY H 313 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   MET H 315 " --> pdb=" O   HIS H 341 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   VAL H 343 " --> pdb=" O   MET H 315 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL H 317 " --> pdb=" O   VAL H 343 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   LEU H 345 " --> pdb=" O   VAL H 317 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   MET H 319 " --> pdb=" O   LEU H 345 " (cutoff:3.500A)
      removed outlier: 8.414A  pdb=" N   HIS H 368 " --> pdb=" O   VAL H 340 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   THR H 342 " --> pdb=" O   HIS H 368 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   PHE H 370 " --> pdb=" O   THR H 342 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   VAL H 344 " --> pdb=" O   PHE H 370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 423 through 425
    Processing sheet with id=AA5, first strand: chain 'H' and resid 452 through 456
      removed outlier: 6.937A  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
      removed outlier: 3.892A  pdb=" N   LYS H 495 " --> pdb=" O   VAL H 479 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 511 through 513
      removed outlier: 6.609A  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: 3.744A  pdb=" N   LYS H 572 " --> pdb=" O   GLU H 581 " (cutoff:3.500A)
      removed outlier: 3.653A  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: 4.187A  pdb=" N   LYS H 602 " --> pdb=" O   GLN H 612 " (cutoff:3.500A)
      removed outlier: 3.742A  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
      removed outlier: 3.569A  pdb=" N   THR H 696 " --> pdb=" O   VAL H 703 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 717 through 720
      removed outlier: 3.897A  pdb=" N   THR H 727 " --> pdb=" O   SER H 719 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 744 through 749
      removed outlier: 3.644A  pdb=" N   GLY H 749 " --> pdb=" O   SER H 753 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'H' and resid 787 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: 6.310A  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 77 through 81
    Processing sheet with id=AC2, first strand: chain 'L' and resid 83 through 84
    Processing sheet with id=AC3, first strand: chain 'L' and resid 103 through 107
      removed outlier: 4.674A  pdb=" N   GLN L 124 " --> pdb=" O   ILE L 172 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   LEU L 170 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'L' and resid 103 through 107
      removed outlier: 17.105A  pdb=" N   GLN L 124 " --> pdb=" O   ALA L 271 " (cutoff:3.500A)
      removed outlier: 13.055A  pdb=" N   ALA L 271 " --> pdb=" O   GLN L 124 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE L 126 " --> pdb=" O   ILE L 269 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ILE L 269 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LEU L 240 " --> pdb=" O   LEU L 232 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   PHE L 230 " --> pdb=" O   TYR L 242 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   HIS L 229 " --> pdb=" O   VAL L 193 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'L' and resid 140 through 143
      removed outlier: 3.595A  pdb=" N   THR L 149 " --> pdb=" O   GLU L 141 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   MET L 147 " --> pdb=" O   ALA L 143 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'L' and resid 206 through 212
      removed outlier: 4.437A  pdb=" N   SER L 206 " --> pdb=" O   LEU L 221 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU L 221 " --> pdb=" O   SER L 206 " (cutoff:3.500A)

    238 hydrogen bonds defined for protein.
    618 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: 1.65

  Time building geometry restraints manager: 0.80 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: 2794
        1.34 -     1.46: 2110
        1.46 -     1.58: 3851
        1.58 -     1.70: 0
        1.70 -     1.82: 106
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" N   ASN H 752 "
       pdb=" CA  ASN H 752 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.55e+00
  bond pdb=" N   ASP H 768 "
       pdb=" CA  ASP H 768 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.16e-02 7.43e+03 5.81e+00
  bond pdb=" N   SER H 767 "
       pdb=" CA  SER H 767 "
    ideal  model  delta    sigma   weight residual
    1.456  1.483 -0.027 1.23e-02 6.61e+03 4.89e+00
  bond pdb=" N   ASN H 769 "
       pdb=" CA  ASN H 769 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.20e-02 6.94e+03 4.21e+00
  bond pdb=" N   ASN H 750 "
       pdb=" CA  ASN H 750 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 3.99e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11792
        1.80 -     3.61: 169
        3.61 -     5.41: 19
        5.41 -     7.22: 4
        7.22 -     9.02: 1
  Bond angle restraints: 11985
  Sorted by residual:
  angle pdb=" CA  ASP H 751 "
        pdb=" C   ASP H 751 "
        pdb=" O   ASP H 751 "
      ideal   model   delta    sigma   weight residual
     122.51  117.95    4.56 1.34e+00 5.57e-01 1.16e+01
  angle pdb=" CA  LEU H 231 "
        pdb=" CB  LEU H 231 "
        pdb=" CG  LEU H 231 "
      ideal   model   delta    sigma   weight residual
     116.30  125.32   -9.02 3.50e+00 8.16e-02 6.64e+00
  angle pdb=" N   ASN H 750 "
        pdb=" CA  ASN H 750 "
        pdb=" C   ASN H 750 "
      ideal   model   delta    sigma   weight residual
     110.80  105.42    5.38 2.13e+00 2.20e-01 6.37e+00
  angle pdb=" CA  ASN H 769 "
        pdb=" C   ASN H 769 "
        pdb=" O   ASN H 769 "
      ideal   model   delta    sigma   weight residual
     120.90  118.21    2.69 1.07e+00 8.73e-01 6.34e+00
  angle pdb=" O   ASP H 768 "
        pdb=" C   ASP H 768 "
        pdb=" N   ASN H 769 "
      ideal   model   delta    sigma   weight residual
     122.08  124.70   -2.62 1.07e+00 8.73e-01 6.00e+00
  ... (remaining 11980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4839
       17.95 -    35.89: 595
       35.89 -    53.84: 154
       53.84 -    71.78: 44
       71.78 -    89.73: 18
  Dihedral angle restraints: 5650
    sinusoidal: 2481
      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  176.18  -83.18     1      1.00e+01 1.00e-02 8.46e+01
  dihedral pdb=" CB  CYS H 592 "
           pdb=" SG  CYS H 592 "
           pdb=" SG  CYS H 630 "
           pdb=" CB  CYS H 630 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.74   63.74     1      1.00e+01 1.00e-02 5.35e+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   31.95   61.05     1      1.00e+01 1.00e-02 4.95e+01
  ... (remaining 5647 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 926
       0.036 -    0.072: 293
       0.072 -    0.108: 94
       0.108 -    0.144: 28
       0.144 -    0.180: 3
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" C1  NAG H 901 "
            pdb=" ND2 ASN H 468 "
            pdb=" C2  NAG H 901 "
            pdb=" O5  NAG H 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.10e-01
  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   -2.22   -0.18 2.00e-01 2.50e+01 7.77e-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   -2.25   -0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1341 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP L 223 "   -0.034 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO L 224 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO L 224 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L 224 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 122 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO H 123 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO H 123 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 123 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP H 545 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.12e+00
        pdb=" CG  ASP H 545 "    0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASP H 545 "   -0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP H 545 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 315
        2.71 -     3.26: 8733
        3.26 -     3.80: 13807
        3.80 -     4.35: 17341
        4.35 -     4.90: 28616
  Nonbonded interactions: 68812
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 227 "
            pdb=" OG  SER H 230 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG1 THR H 186 "
            pdb=" O   CYS H 580 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG L  68 "
            pdb=" OH  TYR L 151 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   LYS L 222 "
            pdb=" OG1 THR L 225 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASP H 283 "
            pdb=" ND2 ASN H 287 "
     model   vdw
     2.254 3.120
  ... (remaining 68807 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:             1.150
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.190
  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:   11.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
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      :  0.002   0.036   8908  Z= 0.127
  Angle     :  0.552   9.020  12092  Z= 0.296
  Chirality :  0.041   0.180   1344
  Planarity :  0.003   0.050   1531
  Dihedral  : 16.909  89.731   3516
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 24.22 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.26), residues: 1066
  helix: -0.75 (0.52), residues: 104
  sheet: -0.08 (0.32), residues: 262
  loop : -0.22 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H 335 
 TYR   0.008   0.001   TYR L 231 
 PHE   0.013   0.001   PHE H 327 
 TRP   0.012   0.001   TRP L 223 
 HIS   0.003   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8861)
  covalent geometry    : angle       0.54313 (11985)
  SS BOND              : bond        0.00239 (   34)
  SS BOND              : angle       0.90022 (   68)
  hydrogen bonds       : bond        0.24585 (  211)
  hydrogen bonds       : angle       9.40507 (  618)
  link_ALPHA1-2        : bond        0.00251 (    2)
  link_ALPHA1-2        : angle       1.37571 (    6)
  link_ALPHA1-3        : bond        0.00307 (    1)
  link_ALPHA1-3        : angle       1.54176 (    3)
  link_ALPHA1-6        : bond        0.00736 (    1)
  link_ALPHA1-6        : angle       1.42287 (    3)
  link_BETA1-4         : bond        0.00426 (    4)
  link_BETA1-4         : angle       1.73134 (   12)
  link_NAG-ASN         : bond        0.00235 (    5)
  link_NAG-ASN         : angle       1.47436 (   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
  123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  106 ASP cc_start: 0.8410 (t0) cc_final: 0.8033 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 118
  average time/residue: 0.0727
  time to fit residues: 12.7794
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  705 GLN
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
H 234 ASN
H 729 HIS
H 741 ASN
L  32 ASN
L  51 GLN
L  65 ASN
** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.111729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.083758 restraints weight = 21623.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086507 restraints weight = 11346.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.088246 restraints weight = 7557.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.089224 restraints weight = 5920.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.089555 restraints weight = 5150.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.0886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8908  Z= 0.139
  Angle     :  0.557  10.278  12092  Z= 0.289
  Chirality :  0.044   0.177   1344
  Planarity :  0.004   0.050   1531
  Dihedral  :  7.720  58.747   1469
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.22 %
    Favored  : 76.40 %
  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: -0.25 (0.26), residues: 1066
  helix: -0.61 (0.49), residues: 117
  sheet:  0.36 (0.35), residues: 232
  loop : -0.22 (0.24), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 347 
 TYR   0.012   0.001   TYR H 269 
 PHE   0.015   0.001   PHE H  64 
 TRP   0.012   0.001   TRP L 223 
 HIS   0.009   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8861)
  covalent geometry    : angle       0.54336 (11985)
  SS BOND              : bond        0.00232 (   34)
  SS BOND              : angle       1.01398 (   68)
  hydrogen bonds       : bond        0.04467 (  211)
  hydrogen bonds       : angle       6.49597 (  618)
  link_ALPHA1-2        : bond        0.00089 (    2)
  link_ALPHA1-2        : angle       1.53595 (    6)
  link_ALPHA1-3        : bond        0.00805 (    1)
  link_ALPHA1-3        : angle       1.41701 (    3)
  link_ALPHA1-6        : bond        0.00521 (    1)
  link_ALPHA1-6        : angle       1.36716 (    3)
  link_BETA1-4         : bond        0.00475 (    4)
  link_BETA1-4         : angle       2.48414 (   12)
  link_NAG-ASN         : bond        0.00232 (    5)
  link_NAG-ASN         : angle       1.63388 (   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
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  106 ASP cc_start: 0.8720 (t0) cc_final: 0.8507 (t0)
  outliers start: 23
  outliers final: 11
  residues processed: 130
  average time/residue: 0.0661
  time to fit residues: 12.6690
Evaluate side-chains
  106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  729 HIS
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue   78 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 77 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   overall best weight:    3.5586

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN
** L 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 188 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 = 0.3655 r_free = 0.3655 target = 0.108857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.083486 restraints weight = 21715.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.083330 restraints weight = 14306.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.084240 restraints weight = 9933.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.084844 restraints weight = 8047.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.085019 restraints weight = 7506.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8908  Z= 0.235
  Angle     :  0.624  12.658  12092  Z= 0.321
  Chirality :  0.045   0.170   1344
  Planarity :  0.004   0.047   1531
  Dihedral  :  7.434  59.339   1466
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 20.81 %
    Favored  : 75.16 %
  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: -0.60 (0.25), residues: 1066
  helix: -0.73 (0.49), residues: 117
  sheet: -0.15 (0.32), residues: 240
  loop : -0.38 (0.24), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.016   0.002   TYR L 231 
 PHE   0.021   0.002   PHE H 258 
 TRP   0.014   0.002   TRP L 223 
 HIS   0.007   0.001   HIS H 729 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 8861)
  covalent geometry    : angle       0.60820 (11985)
  SS BOND              : bond        0.00510 (   34)
  SS BOND              : angle       1.27794 (   68)
  hydrogen bonds       : bond        0.03971 (  211)
  hydrogen bonds       : angle       6.09233 (  618)
  link_ALPHA1-2        : bond        0.00132 (    2)
  link_ALPHA1-2        : angle       1.81593 (    6)
  link_ALPHA1-3        : bond        0.00615 (    1)
  link_ALPHA1-3        : angle       1.74002 (    3)
  link_ALPHA1-6        : bond        0.00474 (    1)
  link_ALPHA1-6        : angle       1.44848 (    3)
  link_BETA1-4         : bond        0.00507 (    4)
  link_BETA1-4         : angle       2.43567 (   12)
  link_NAG-ASN         : bond        0.00246 (    5)
  link_NAG-ASN         : angle       1.93368 (   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
  144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 105
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  349 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8683 (tptm)
REVERT: H  531 MET cc_start: 0.8061 (mmm) cc_final: 0.7817 (mmm)
REVERT: L  106 ASP cc_start: 0.8811 (t0) cc_final: 0.8557 (t0)
REVERT: L  119 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8675 (m-40)
  outliers start: 39
  outliers final: 22
  residues processed: 135
  average time/residue: 0.0727
  time to fit residues: 14.3774
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  757 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  110 ASP
Chi-restraints excluded: chain L residue  119 ASN
Chi-restraints excluded: chain L residue  171 ILE
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 26 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
L 176 ASN
** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 188 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.082985 restraints weight = 22159.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.085277 restraints weight = 10918.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.087147 restraints weight = 7439.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.087331 restraints weight = 6207.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.087181 restraints weight = 5540.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8908  Z= 0.155
  Angle     :  0.567  12.203  12092  Z= 0.290
  Chirality :  0.044   0.193   1344
  Planarity :  0.003   0.051   1531
  Dihedral  :  6.996  59.884   1466
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.12 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.25), residues: 1066
  helix: -0.42 (0.52), residues: 111
  sheet: -0.13 (0.33), residues: 242
  loop : -0.39 (0.23), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.027   0.001   TYR L 231 
 PHE   0.017   0.001   PHE H 258 
 TRP   0.018   0.001   TRP L 223 
 HIS   0.005   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8861)
  covalent geometry    : angle       0.55377 (11985)
  SS BOND              : bond        0.00276 (   34)
  SS BOND              : angle       1.04872 (   68)
  hydrogen bonds       : bond        0.03362 (  211)
  hydrogen bonds       : angle       5.77606 (  618)
  link_ALPHA1-2        : bond        0.00036 (    2)
  link_ALPHA1-2        : angle       1.61557 (    6)
  link_ALPHA1-3        : bond        0.00883 (    1)
  link_ALPHA1-3        : angle       1.47726 (    3)
  link_ALPHA1-6        : bond        0.00791 (    1)
  link_ALPHA1-6        : angle       1.27441 (    3)
  link_BETA1-4         : bond        0.00510 (    4)
  link_BETA1-4         : angle       2.22229 (   12)
  link_NAG-ASN         : bond        0.00209 (    5)
  link_NAG-ASN         : angle       1.89556 (   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
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 104
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  349 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8565 (tptm)
REVERT: H  531 MET cc_start: 0.8180 (mmm) cc_final: 0.7974 (mmm)
REVERT: H  656 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7988 (tppp)
REVERT: L  106 ASP cc_start: 0.8782 (t0) cc_final: 0.8549 (t0)
REVERT: L  108 GLU cc_start: 0.8226 (mp0) cc_final: 0.7894 (pm20)
  outliers start: 39
  outliers final: 26
  residues processed: 137
  average time/residue: 0.0726
  time to fit residues: 14.6454
Evaluate side-chains
  122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  249 ASP
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0010
   chunk 32 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    3.3792

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

Flipped N/Q/H residues before XYZ refinement:
L  51 GLN
L 119 ASN
** L 187 ASN ** 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 = 0.3631 r_free = 0.3631 target = 0.107278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.080962 restraints weight = 22052.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.082514 restraints weight = 11679.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084562 restraints weight = 8333.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.084666 restraints weight = 6568.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.084506 restraints weight = 6126.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8908  Z= 0.229
  Angle     :  0.625  13.572  12092  Z= 0.317
  Chirality :  0.045   0.185   1344
  Planarity :  0.004   0.049   1531
  Dihedral  :  7.093  59.896   1466
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.70 %
    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: -0.62 (0.25), residues: 1066
  helix: -0.50 (0.52), residues: 111
  sheet: -0.12 (0.33), residues: 230
  loop : -0.46 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 347 
 TYR   0.012   0.001   TYR L 103 
 PHE   0.018   0.002   PHE H  64 
 TRP   0.015   0.002   TRP H 435 
 HIS   0.005   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00511 ( 8861)
  covalent geometry    : angle       0.61045 (11985)
  SS BOND              : bond        0.00475 (   34)
  SS BOND              : angle       1.20418 (   68)
  hydrogen bonds       : bond        0.03515 (  211)
  hydrogen bonds       : angle       5.68337 (  618)
  link_ALPHA1-2        : bond        0.00153 (    2)
  link_ALPHA1-2        : angle       1.80858 (    6)
  link_ALPHA1-3        : bond        0.00767 (    1)
  link_ALPHA1-3        : angle       1.84845 (    3)
  link_ALPHA1-6        : bond        0.00502 (    1)
  link_ALPHA1-6        : angle       1.21921 (    3)
  link_BETA1-4         : bond        0.00550 (    4)
  link_BETA1-4         : angle       2.30971 (   12)
  link_NAG-ASN         : bond        0.00213 (    5)
  link_NAG-ASN         : angle       2.00243 (   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
  149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 102
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8001 (ptpp)
REVERT: H  186 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7910 (p)
REVERT: H  349 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8610 (tptm)
REVERT: H  656 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7939 (tppt)
REVERT: H  729 HIS cc_start: 0.8371 (m-70) cc_final: 0.8119 (m90)
REVERT: L   14 LYS cc_start: 0.6743 (tptp) cc_final: 0.6392 (mttt)
REVERT: L  106 ASP cc_start: 0.8855 (t0) cc_final: 0.8581 (t0)
  outliers start: 47
  outliers final: 37
  residues processed: 140
  average time/residue: 0.0833
  time to fit residues: 16.7259
Evaluate side-chains
  134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 93
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  412 CYS
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  456 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  720 MET
Chi-restraints excluded: chain H residue  757 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  110 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  171 ILE
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  207 THR
Chi-restraints excluded: chain L residue  249 ASP
Chi-restraints excluded: chain L residue  262 THR
Chi-restraints excluded: chain L residue  264 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0170
   chunk 53 optimal weight:    0.4980
   chunk 14 optimal weight:   10.0000
   chunk 96 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 75 optimal weight:    0.0270
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
L  51 GLN
** L 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.110182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084409 restraints weight = 21860.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.085799 restraints weight = 11695.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.086420 restraints weight = 8250.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.087511 restraints weight = 7449.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.087556 restraints weight = 6516.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8908  Z= 0.109
  Angle     :  0.587  14.377  12092  Z= 0.297
  Chirality :  0.044   0.212   1344
  Planarity :  0.003   0.052   1531
  Dihedral  :  6.447  56.976   1466
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.95 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.25), residues: 1066
  helix: -0.43 (0.54), residues: 105
  sheet: -0.08 (0.33), residues: 233
  loop : -0.31 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H 347 
 TYR   0.031   0.001   TYR L 231 
 PHE   0.015   0.001   PHE H 258 
 TRP   0.020   0.001   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8861)
  covalent geometry    : angle       0.56783 (11985)
  SS BOND              : bond        0.00239 (   34)
  SS BOND              : angle       1.60063 (   68)
  hydrogen bonds       : bond        0.03096 (  211)
  hydrogen bonds       : angle       5.44965 (  618)
  link_ALPHA1-2        : bond        0.00225 (    2)
  link_ALPHA1-2        : angle       1.58698 (    6)
  link_ALPHA1-3        : bond        0.01232 (    1)
  link_ALPHA1-3        : angle       1.36992 (    3)
  link_ALPHA1-6        : bond        0.01043 (    1)
  link_ALPHA1-6        : angle       1.13660 (    3)
  link_BETA1-4         : bond        0.00544 (    4)
  link_BETA1-4         : angle       2.00094 (   12)
  link_NAG-ASN         : bond        0.00302 (    5)
  link_NAG-ASN         : angle       1.85174 (   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
  147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 108
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7769 (ptpp)
REVERT: H  349 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8618 (tptm)
REVERT: H  414 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8288 (mmm)
REVERT: H  531 MET cc_start: 0.8182 (mmm) cc_final: 0.7587 (mmm)
REVERT: H  656 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7998 (tppp)
REVERT: L   14 LYS cc_start: 0.6699 (tptp) cc_final: 0.6295 (mttt)
REVERT: L  106 ASP cc_start: 0.8717 (t0) cc_final: 0.8507 (t0)
REVERT: L  108 GLU cc_start: 0.8247 (mp0) cc_final: 0.7915 (pm20)
  outliers start: 39
  outliers final: 26
  residues processed: 140
  average time/residue: 0.0847
  time to fit residues: 17.1071
Evaluate side-chains
  123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  276 THR
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  414 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  544 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  188 GLN
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 56 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 29 optimal weight:    0.2980
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:   20.0000
   chunk 102 optimal weight:    0.0670
   overall best weight:    2.8122

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN
** L 187 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.107832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.082140 restraints weight = 22283.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.083346 restraints weight = 10825.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.083647 restraints weight = 8035.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.084275 restraints weight = 8209.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.084153 restraints weight = 6800.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8908  Z= 0.197
  Angle     :  0.607  14.707  12092  Z= 0.308
  Chirality :  0.045   0.182   1344
  Planarity :  0.003   0.051   1531
  Dihedral  :  6.664  59.495   1466
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 22.05 %
    Favored  : 72.98 %
  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 (0.25), residues: 1066
  helix: -0.39 (0.54), residues: 105
  sheet: -0.18 (0.33), residues: 239
  loop : -0.36 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.011   0.001   TYR L 103 
 PHE   0.015   0.001   PHE H  64 
 TRP   0.012   0.002   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 8861)
  covalent geometry    : angle       0.59295 (11985)
  SS BOND              : bond        0.00318 (   34)
  SS BOND              : angle       1.22891 (   68)
  hydrogen bonds       : bond        0.03289 (  211)
  hydrogen bonds       : angle       5.58853 (  618)
  link_ALPHA1-2        : bond        0.00160 (    2)
  link_ALPHA1-2        : angle       1.76704 (    6)
  link_ALPHA1-3        : bond        0.00612 (    1)
  link_ALPHA1-3        : angle       1.63323 (    3)
  link_ALPHA1-6        : bond        0.00789 (    1)
  link_ALPHA1-6        : angle       1.22328 (    3)
  link_BETA1-4         : bond        0.00546 (    4)
  link_BETA1-4         : angle       2.20521 (   12)
  link_NAG-ASN         : bond        0.00211 (    5)
  link_NAG-ASN         : angle       1.93464 (   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
  141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 93
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7992 (ptpp)
REVERT: H  186 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.7869 (p)
REVERT: H  349 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8720 (tptm)
REVERT: H  414 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8263 (mmm)
REVERT: H  531 MET cc_start: 0.8316 (mmm) cc_final: 0.7869 (mmm)
REVERT: H  656 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7880 (tppt)
REVERT: L   14 LYS cc_start: 0.6836 (tptp) cc_final: 0.6349 (mttt)
REVERT: L  106 ASP cc_start: 0.8813 (t0) cc_final: 0.8576 (t0)
  outliers start: 48
  outliers final: 34
  residues processed: 132
  average time/residue: 0.0778
  time to fit residues: 14.9669
Evaluate side-chains
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 87
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  412 CYS
Chi-restraints excluded: chain H residue  414 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  456 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  544 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  110 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  262 THR
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 72 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0570
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN
** L 187 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.108624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084181 restraints weight = 21821.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.083684 restraints weight = 13520.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.084224 restraints weight = 10303.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.084836 restraints weight = 8700.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.085034 restraints weight = 7986.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8908  Z= 0.144
  Angle     :  0.583  14.695  12092  Z= 0.295
  Chirality :  0.045   0.197   1344
  Planarity :  0.003   0.052   1531
  Dihedral  :  6.430  58.531   1466
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.26 %
    Favored  : 72.88 %
  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: -0.36 (0.54), residues: 105
  sheet: -0.16 (0.33), residues: 239
  loop : -0.33 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.020   0.001   TYR L  53 
 PHE   0.013   0.001   PHE H 258 
 TRP   0.013   0.001   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8861)
  covalent geometry    : angle       0.56999 (11985)
  SS BOND              : bond        0.00279 (   34)
  SS BOND              : angle       1.10112 (   68)
  hydrogen bonds       : bond        0.03056 (  211)
  hydrogen bonds       : angle       5.52339 (  618)
  link_ALPHA1-2        : bond        0.00040 (    2)
  link_ALPHA1-2        : angle       1.64574 (    6)
  link_ALPHA1-3        : bond        0.00909 (    1)
  link_ALPHA1-3        : angle       1.46091 (    3)
  link_ALPHA1-6        : bond        0.00900 (    1)
  link_ALPHA1-6        : angle       1.13407 (    3)
  link_BETA1-4         : bond        0.00525 (    4)
  link_BETA1-4         : angle       2.10535 (   12)
  link_NAG-ASN         : bond        0.00220 (    5)
  link_NAG-ASN         : angle       1.91537 (   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
  143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7970 (ptpp)
REVERT: H  349 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8718 (tptm)
REVERT: H  414 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8254 (mmm)
REVERT: H  531 MET cc_start: 0.8316 (mmm) cc_final: 0.7883 (mmm)
REVERT: H  656 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7983 (tppp)
REVERT: L   14 LYS cc_start: 0.6709 (tptp) cc_final: 0.6260 (mttt)
REVERT: L  108 GLU cc_start: 0.8273 (mp0) cc_final: 0.7939 (pm20)
  outliers start: 47
  outliers final: 36
  residues processed: 132
  average time/residue: 0.0777
  time to fit residues: 14.9249
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  241 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  412 CYS
Chi-restraints excluded: chain H residue  414 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  544 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  757 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  110 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  249 ASP
Chi-restraints excluded: chain L residue  262 THR
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 48 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN
** L 187 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.108284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.082833 restraints weight = 21883.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.083678 restraints weight = 10950.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.084338 restraints weight = 8486.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.084735 restraints weight = 7810.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.084911 restraints weight = 7181.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8908  Z= 0.152
  Angle     :  0.593  15.331  12092  Z= 0.302
  Chirality :  0.045   0.193   1344
  Planarity :  0.003   0.052   1531
  Dihedral  :  6.349  58.296   1466
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.46 %
    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: -0.50 (0.25), residues: 1066
  helix: -0.41 (0.54), residues: 105
  sheet: -0.23 (0.33), residues: 249
  loop : -0.30 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 347 
 TYR   0.020   0.001   TYR L  53 
 PHE   0.013   0.001   PHE H  64 
 TRP   0.014   0.001   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8861)
  covalent geometry    : angle       0.58136 (11985)
  SS BOND              : bond        0.00296 (   34)
  SS BOND              : angle       1.03042 (   68)
  hydrogen bonds       : bond        0.03022 (  211)
  hydrogen bonds       : angle       5.54938 (  618)
  link_ALPHA1-2        : bond        0.00039 (    2)
  link_ALPHA1-2        : angle       1.65393 (    6)
  link_ALPHA1-3        : bond        0.00841 (    1)
  link_ALPHA1-3        : angle       1.48564 (    3)
  link_ALPHA1-6        : bond        0.00887 (    1)
  link_ALPHA1-6        : angle       1.12521 (    3)
  link_BETA1-4         : bond        0.00520 (    4)
  link_BETA1-4         : angle       2.10610 (   12)
  link_NAG-ASN         : bond        0.00200 (    5)
  link_NAG-ASN         : angle       1.90429 (   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
  139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 92
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7901 (ptpp)
REVERT: H  186 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7843 (p)
REVERT: H  349 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8782 (tptm)
REVERT: H  414 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8302 (mmm)
REVERT: H  531 MET cc_start: 0.8401 (mmm) cc_final: 0.8016 (mmm)
REVERT: H  656 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7970 (tppp)
REVERT: L   14 LYS cc_start: 0.6722 (tptp) cc_final: 0.6313 (mttt)
  outliers start: 47
  outliers final: 37
  residues processed: 130
  average time/residue: 0.0824
  time to fit residues: 15.5355
Evaluate side-chains
  131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 89
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  241 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  412 CYS
Chi-restraints excluded: chain H residue  414 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  456 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  544 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  757 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  159 ASP
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  249 ASP
Chi-restraints excluded: chain L residue  262 THR
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 62 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 96 optimal weight:    3.9990
   chunk 98 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 97 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    8.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN
** L 187 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.107479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.082259 restraints weight = 22112.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.083017 restraints weight = 11721.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.083673 restraints weight = 9273.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.084012 restraints weight = 7992.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.084077 restraints weight = 7488.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8908  Z= 0.183
  Angle     :  0.615  15.583  12092  Z= 0.312
  Chirality :  0.045   0.188   1344
  Planarity :  0.003   0.049   1531
  Dihedral  :  6.439  59.224   1466
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 22.67 %
    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: -0.51 (0.25), residues: 1066
  helix: -0.41 (0.53), residues: 105
  sheet: -0.15 (0.33), residues: 235
  loop : -0.35 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.023   0.001   TYR L 231 
 PHE   0.014   0.001   PHE H  64 
 TRP   0.022   0.002   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8861)
  covalent geometry    : angle       0.60235 (11985)
  SS BOND              : bond        0.00305 (   34)
  SS BOND              : angle       1.16040 (   68)
  hydrogen bonds       : bond        0.03075 (  211)
  hydrogen bonds       : angle       5.59440 (  618)
  link_ALPHA1-2        : bond        0.00095 (    2)
  link_ALPHA1-2        : angle       1.69411 (    6)
  link_ALPHA1-3        : bond        0.00755 (    1)
  link_ALPHA1-3        : angle       1.59416 (    3)
  link_ALPHA1-6        : bond        0.00922 (    1)
  link_ALPHA1-6        : angle       1.16821 (    3)
  link_BETA1-4         : bond        0.00511 (    4)
  link_BETA1-4         : angle       2.14641 (   12)
  link_NAG-ASN         : bond        0.00188 (    5)
  link_NAG-ASN         : angle       1.93467 (   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
  141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 96
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   17 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7968 (ptpp)
REVERT: H  186 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.7914 (p)
REVERT: H  349 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8759 (tptm)
REVERT: H  414 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8233 (mmm)
REVERT: H  531 MET cc_start: 0.8409 (mmm) cc_final: 0.8038 (mmm)
REVERT: H  656 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7941 (tppt)
REVERT: H  713 VAL cc_start: 0.7691 (t) cc_final: 0.7240 (p)
REVERT: L   14 LYS cc_start: 0.6735 (tptp) cc_final: 0.6223 (mttt)
  outliers start: 45
  outliers final: 38
  residues processed: 133
  average time/residue: 0.0803
  time to fit residues: 15.4060
Evaluate side-chains
  135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   17 LYS
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  122 VAL
Chi-restraints excluded: chain H residue  186 THR
Chi-restraints excluded: chain H residue  234 ASN
Chi-restraints excluded: chain H residue  238 LEU
Chi-restraints excluded: chain H residue  241 LEU
Chi-restraints excluded: chain H residue  269 TYR
Chi-restraints excluded: chain H residue  308 ASP
Chi-restraints excluded: chain H residue  318 LEU
Chi-restraints excluded: chain H residue  349 LYS
Chi-restraints excluded: chain H residue  395 CYS
Chi-restraints excluded: chain H residue  404 CYS
Chi-restraints excluded: chain H residue  412 CYS
Chi-restraints excluded: chain H residue  414 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  450 CYS
Chi-restraints excluded: chain H residue  456 CYS
Chi-restraints excluded: chain H residue  479 VAL
Chi-restraints excluded: chain H residue  482 CYS
Chi-restraints excluded: chain H residue  493 LYS
Chi-restraints excluded: chain H residue  498 CYS
Chi-restraints excluded: chain H residue  544 CYS
Chi-restraints excluded: chain H residue  564 ILE
Chi-restraints excluded: chain H residue  566 MET
Chi-restraints excluded: chain H residue  629 ILE
Chi-restraints excluded: chain H residue  649 VAL
Chi-restraints excluded: chain H residue  656 LYS
Chi-restraints excluded: chain H residue  669 ASN
Chi-restraints excluded: chain H residue  670 VAL
Chi-restraints excluded: chain H residue  757 VAL
Chi-restraints excluded: chain H residue  788 THR
Chi-restraints excluded: chain H residue  811 CYS
Chi-restraints excluded: chain L residue   45 VAL
Chi-restraints excluded: chain L residue   51 GLN
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  127 LEU
Chi-restraints excluded: chain L residue  159 ASP
Chi-restraints excluded: chain L residue  188 GLN
Chi-restraints excluded: chain L residue  249 ASP
Chi-restraints excluded: chain L residue  262 THR
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 16 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 105 optimal weight:   10.0000
   chunk 41 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
H 729 HIS
L  51 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.108510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.083301 restraints weight = 21884.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.084074 restraints weight = 11021.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.084791 restraints weight = 8661.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.086186 restraints weight = 7556.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.086071 restraints weight = 6732.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8908  Z= 0.134
  Angle     :  0.598  15.886  12092  Z= 0.303
  Chirality :  0.045   0.202   1344
  Planarity :  0.003   0.052   1531
  Dihedral  :  6.201  57.741   1466
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.67 %
    Favored  : 72.57 %
  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: -0.40 (0.54), residues: 105
  sheet: -0.12 (0.33), residues: 235
  loop : -0.30 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 335 
 TYR   0.015   0.001   TYR L  53 
 PHE   0.013   0.001   PHE H 258 
 TRP   0.028   0.002   TRP L 223 
 HIS   0.004   0.001   HIS H  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8861)
  covalent geometry    : angle       0.58617 (11985)
  SS BOND              : bond        0.00287 (   34)
  SS BOND              : angle       1.02361 (   68)
  hydrogen bonds       : bond        0.02915 (  211)
  hydrogen bonds       : angle       5.51062 (  618)
  link_ALPHA1-2        : bond        0.00062 (    2)
  link_ALPHA1-2        : angle       1.62608 (    6)
  link_ALPHA1-3        : bond        0.00968 (    1)
  link_ALPHA1-3        : angle       1.44824 (    3)
  link_ALPHA1-6        : bond        0.01016 (    1)
  link_ALPHA1-6        : angle       1.12774 (    3)
  link_BETA1-4         : bond        0.00531 (    4)
  link_BETA1-4         : angle       2.06246 (   12)
  link_NAG-ASN         : bond        0.00211 (    5)
  link_NAG-ASN         : angle       1.88934 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1386.40 seconds
wall clock time: 24 minutes 48.00 seconds (1488.00 seconds total)