Starting phenix.real_space_refine
on Sun May  3 09:05:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x0d_37975/05_2026/8x0d_37975.cif"
  }
  resolution = 3.5
  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=   0.001 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S     116      5.16       5
     C    7832      2.51       5
     N    2016      2.21       5
     O    2214      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12180
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 768, 6039
          Classifications: {'peptide': 768}
          Link IDs: {'PTRANS': 32, 'TRANS': 735}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 768, 6039
          Classifications: {'peptide': 768}
          Link IDs: {'PTRANS': 32, 'TRANS': 735}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 51
          Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 51
          Unusual residues: {'NAG': 1, 'QUS': 1, 'XQT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.81, per 1000 atoms: 0.23
  Number of scatterers: 12180
  At special positions: 0
  Unit cell: (81.8072, 97.1461, 176.908, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S     116     16.00
     F       2      9.00
     O    2214      8.00
     N    2016      7.00
     C    7832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  99 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 530 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 278 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 381 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 531 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 537 " - pdb=" SG  CYS A 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 552 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 644 " - pdb=" SG  CYS A 733 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  99 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 530 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 278 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 381 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 419 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 531 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 549 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 552 " - pdb=" SG  CYS B 565 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 733 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 210 "
      " NAG B 901 " - " ASN B 210 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 466.9 milliseconds
  

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2864

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 16 sheets defined
      49.7% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 82
      removed outlier: 3.674A  pdb=" N   GLU A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
    Processing helix  chain 'A' and resid 151 through 163
    Processing helix  chain 'A' and resid 164 through 166
      No H-bonds generated for 'chain 'A' and resid 164 through 166'
    Processing helix  chain 'A' and resid 176 through 181
    Processing helix  chain 'A' and resid 194 through 209
      removed outlier: 4.131A  pdb=" N   GLN A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   TYR A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 238
    Processing helix  chain 'A' and resid 253 through 266
    Processing helix  chain 'A' and resid 279 through 293
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.582A  pdb=" N   GLU A 320 " --> pdb=" O   TYR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
    Processing helix  chain 'A' and resid 354 through 363
    Processing helix  chain 'A' and resid 396 through 419
      removed outlier: 3.529A  pdb=" N   CYS A 419 " --> pdb=" O   GLN A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
      removed outlier: 3.574A  pdb=" N   LYS A 430 " --> pdb=" O   ASP A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 444
    Processing helix  chain 'A' and resid 577 through 604
    Processing helix  chain 'A' and resid 607 through 611
      removed outlier: 3.566A  pdb=" N   LYS A 611 " --> pdb=" O   PRO A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 636
      removed outlier: 3.754A  pdb=" N   THR A 632 " --> pdb=" O   GLY A 628 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 675
      removed outlier: 3.504A  pdb=" N   LEU A 646 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      Proline residue:  A 655  - end of helix
      removed outlier: 3.817A  pdb=" N   ALA A 661 " --> pdb=" O   MET A 657 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   THR A 664 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 715
    Processing helix  chain 'A' and resid 736 through 762
      Proline residue:  A 743  - end of helix
    Processing helix  chain 'A' and resid 769 through 788
      removed outlier: 4.331A  pdb=" N   TYR A 773 " --> pdb=" O   ASN A 769 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE A 788 " --> pdb=" O   ILE A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 794
      removed outlier: 3.806A  pdb=" N   GLY A 794 " --> pdb=" O   PRO A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 817
      removed outlier: 3.704A  pdb=" N   THR A 801 " --> pdb=" O   TYR A 797 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 813 " --> pdb=" O   SER A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 827
    Processing helix  chain 'B' and resid 65 through 82
      removed outlier: 3.674A  pdb=" N   GLU B  77 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
    Processing helix  chain 'B' and resid 151 through 163
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'B' and resid 176 through 181
    Processing helix  chain 'B' and resid 194 through 209
      removed outlier: 4.120A  pdb=" N   GLN B 198 " --> pdb=" O   SER B 194 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR B 209 " --> pdb=" O   ILE B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 239
    Processing helix  chain 'B' and resid 253 through 266
    Processing helix  chain 'B' and resid 279 through 293
    Processing helix  chain 'B' and resid 317 through 321
    Processing helix  chain 'B' and resid 334 through 342
      removed outlier: 3.508A  pdb=" N   ASP B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 363
    Processing helix  chain 'B' and resid 396 through 419
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 433 through 444
    Processing helix  chain 'B' and resid 560 through 563
      removed outlier: 3.704A  pdb=" N   THR B 563 " --> pdb=" O   ASP B 560 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 560 through 563'
    Processing helix  chain 'B' and resid 577 through 604
    Processing helix  chain 'B' and resid 616 through 636
      removed outlier: 4.304A  pdb=" N   LEU B 622 " --> pdb=" O   CYS B 618 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   PHE B 633 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   CYS B 634 " --> pdb=" O   LEU B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 675
      removed outlier: 3.756A  pdb=" N   ARG B 648 " --> pdb=" O   CYS B 644 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE B 649 " --> pdb=" O   TYR B 645 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
    Processing helix  chain 'B' and resid 691 through 715
      removed outlier: 3.935A  pdb=" N   VAL B 695 " --> pdb=" O   CYS B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 761
      Proline residue:  B 743  - end of helix
      removed outlier: 3.607A  pdb=" N   LYS B 760 " --> pdb=" O   PHE B 756 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 769 through 788
      removed outlier: 4.070A  pdb=" N   TYR B 773 " --> pdb=" O   ASN B 769 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE B 788 " --> pdb=" O   ILE B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 788 through 793
    Processing helix  chain 'B' and resid 797 through 817
      removed outlier: 3.531A  pdb=" N   ALA B 810 " --> pdb=" O   VAL B 806 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   THR B 811 " --> pdb=" O   SER B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 818 through 827
    Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 97
      removed outlier: 7.372A  pdb=" N   ILE A  36 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   GLY A 145 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 8.643A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 248
      removed outlier: 7.833A  pdb=" N   VAL A 214 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   SER A 245 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA A 216 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LYS A 247 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
      removed outlier: 5.122A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR A 219 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 329
      removed outlier: 6.665A  pdb=" N   TYR A 466 " --> pdb=" O   SER A 486 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   SER A 486 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ILE A 468 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   TYR A 478 " --> pdb=" O   MET A 474 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 447
      removed outlier: 3.583A  pdb=" N   PHE A 446 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 528
      removed outlier: 4.141A  pdb=" N   LYS A 525 " --> pdb=" O   CYS A 531 " (cutoff:3.500A)
      removed outlier: 9.041A  pdb=" N   CYS A 531 " --> pdb=" O   LYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 545
      removed outlier: 3.865A  pdb=" N   PHE A 544 " --> pdb=" O   THR A 548 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   THR A 548 " --> pdb=" O   PHE A 544 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 558
    Processing sheet with id=AA8, first strand: chain 'A' and resid 719 through 722
    Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.275A  pdb=" N   ILE B  35 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   GLU B  94 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE B  37 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   ALA B  39 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 7.312A  pdb=" N   ILE B  36 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLY B 145 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 8.622A  pdb=" N   ILE B 170 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 241 through 248
      removed outlier: 7.854A  pdb=" N   VAL B 214 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   SER B 245 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA B 216 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   LYS B 247 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   HIS B 218 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR B 219 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 329
      removed outlier: 6.439A  pdb=" N   ASN B 470 " --> pdb=" O   ASN B 483 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   ASN B 483 " --> pdb=" O   ASN B 470 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LYS B 472 " --> pdb=" O   TYR B 481 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   TYR B 481 " --> pdb=" O   LYS B 472 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   MET B 474 " --> pdb=" O   PHE B 479 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   PHE B 479 " --> pdb=" O   MET B 474 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 447
    Processing sheet with id=AB4, first strand: chain 'B' and resid 520 through 523
    Processing sheet with id=AB5, first strand: chain 'B' and resid 541 through 545
      removed outlier: 5.337A  pdb=" N   VAL B 543 " --> pdb=" O   LYS B 550 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   LYS B 550 " --> pdb=" O   VAL B 543 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 556 through 558
    Processing sheet with id=AB7, first strand: chain 'B' and resid 719 through 722
      removed outlier: 3.521A  pdb=" N   ASP B 722 " --> pdb=" O   TYR B 730 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR B 730 " --> pdb=" O   ASP B 722 " (cutoff:3.500A)

    612 hydrogen bonds defined for protein.
    1776 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: 2.24

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1989
        1.32 -     1.45: 3341
        1.45 -     1.57: 6960
        1.57 -     1.70: 0
        1.70 -     1.83: 168
  Bond restraints: 12458
  Sorted by residual:
  bond pdb=" CA  SER B 304 "
       pdb=" CB  SER B 304 "
    ideal  model  delta    sigma   weight residual
    1.537  1.500  0.037 1.45e-02 4.76e+03 6.51e+00
  bond pdb=" CA  SER A 304 "
       pdb=" CB  SER A 304 "
    ideal  model  delta    sigma   weight residual
    1.537  1.502  0.035 1.45e-02 4.76e+03 5.68e+00
  bond pdb=" CA  SER A 462 "
       pdb=" CB  SER A 462 "
    ideal  model  delta    sigma   weight residual
    1.537  1.506  0.031 1.38e-02 5.25e+03 5.07e+00
  bond pdb=" CA  ALA A 766 "
       pdb=" CB  ALA A 766 "
    ideal  model  delta    sigma   weight residual
    1.539  1.510  0.029 1.36e-02 5.41e+03 4.65e+00
  bond pdb=" CA  SER A 152 "
       pdb=" CB  SER A 152 "
    ideal  model  delta    sigma   weight residual
    1.529  1.495  0.034 1.62e-02 3.81e+03 4.35e+00
  ... (remaining 12453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 16143
        2.18 -     4.37: 720
        4.37 -     6.55: 16
        6.55 -     8.73: 3
        8.73 -    10.92: 2
  Bond angle restraints: 16884
  Sorted by residual:
  angle pdb=" OD1 ASN B 210 "
        pdb=" CG  ASN B 210 "
        pdb=" ND2 ASN B 210 "
      ideal   model   delta    sigma   weight residual
     122.60  127.30   -4.70 1.00e+00 1.00e+00 2.21e+01
  angle pdb=" C   CYS A 644 "
        pdb=" CA  CYS A 644 "
        pdb=" CB  CYS A 644 "
      ideal   model   delta    sigma   weight residual
     110.96  104.17    6.79 1.54e+00 4.22e-01 1.95e+01
  angle pdb=" CA  ASP A 495 "
        pdb=" CB  ASP A 495 "
        pdb=" CG  ASP A 495 "
      ideal   model   delta    sigma   weight residual
     112.60  116.87   -4.27 1.00e+00 1.00e+00 1.83e+01
  angle pdb=" CA  ASP A 309 "
        pdb=" CB  ASP A 309 "
        pdb=" CG  ASP A 309 "
      ideal   model   delta    sigma   weight residual
     112.60  116.87   -4.27 1.00e+00 1.00e+00 1.82e+01
  angle pdb=" N   VAL B 191 "
        pdb=" CA  VAL B 191 "
        pdb=" C   VAL B 191 "
      ideal   model   delta    sigma   weight residual
     111.91  108.47    3.44 8.90e-01 1.26e+00 1.50e+01
  ... (remaining 16879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.16: 7185
       31.16 -    62.33: 295
       62.33 -    93.49: 27
       93.49 -   124.66: 8
      124.66 -   155.82: 1
  Dihedral angle restraints: 7516
    sinusoidal: 3048
      harmonic: 4468
  Sorted by residual:
  dihedral pdb=" CB  CYS B  57 "
           pdb=" SG  CYS B  57 "
           pdb=" SG  CYS B  99 "
           pdb=" CB  CYS B  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.07  -82.93     1      1.00e+01 1.00e-02 8.42e+01
  dihedral pdb=" CB  CYS A  57 "
           pdb=" SG  CYS A  57 "
           pdb=" SG  CYS A  99 "
           pdb=" CB  CYS A  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -7.60  -78.40     1      1.00e+01 1.00e-02 7.67e+01
  dihedral pdb=" CB  CYS A 515 "
           pdb=" SG  CYS A 515 "
           pdb=" SG  CYS A 534 "
           pdb=" CB  CYS A 534 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.88  -71.88     1      1.00e+01 1.00e-02 6.61e+01
  ... (remaining 7513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1641
       0.101 -    0.202: 246
       0.202 -    0.303: 3
       0.303 -    0.403: 1
       0.403 -    0.504: 1
  Chirality restraints: 1892
  Sorted by residual:
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A 210 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.90   -0.50 2.00e-01 2.50e+01 6.36e+00
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B 210 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.07   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  THR B 755 "
            pdb=" N   THR B 755 "
            pdb=" C   THR B 755 "
            pdb=" CB  THR B 755 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.29    0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1889 not shown)

  Planarity restraints: 2126
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 901 "    0.100 2.00e-02 2.50e+03   8.18e-02 8.37e+01
        pdb=" C7  NAG B 901 "   -0.028 2.00e-02 2.50e+03
        pdb=" C8  NAG B 901 "    0.075 2.00e-02 2.50e+03
        pdb=" N2  NAG B 901 "   -0.129 2.00e-02 2.50e+03
        pdb=" O7  NAG B 901 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  XQT A 903 "    0.044 2.00e-02 2.50e+03   3.66e-02 1.67e+01
        pdb=" C6  XQT A 903 "   -0.016 2.00e-02 2.50e+03
        pdb=" C7  XQT A 903 "    0.035 2.00e-02 2.50e+03
        pdb=" N1  XQT A 903 "   -0.057 2.00e-02 2.50e+03
        pdb=" O2  XQT A 903 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 310 "    0.246 9.50e-02 1.11e+02   1.10e-01 7.64e+00
        pdb=" NE  ARG A 310 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 310 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 310 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 310 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2123 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2104
        2.78 -     3.31: 12711
        3.31 -     3.84: 20483
        3.84 -     4.37: 23801
        4.37 -     4.90: 40308
  Nonbonded interactions: 99407
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 198 "
            pdb=" OG  SER B 304 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR B 311 "
            pdb=" OD1 ASP B 480 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" N   ASP A 718 "
            pdb=" OD1 ASN A 734 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OH  TYR A 311 "
            pdb=" OD1 ASP A 480 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OE1 GLU A 254 "
            pdb=" NH1 ARG A 292 "
     model   vdw
     2.293 3.120
  ... (remaining 99402 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.420
  Find NCS groups from input model:        0.210
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
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      :  0.007   0.041  12480  Z= 0.447
  Angle     :  1.086  20.238  16930  Z= 0.726
  Chirality :  0.067   0.504   1892
  Planarity :  0.008   0.110   2124
  Dihedral  : 16.318 155.820   4592
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.69 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.48 %
    Favored  : 87.01 %
  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: -1.51 (0.20), residues: 1524
  helix:  0.24 (0.18), residues: 705
  sheet: -1.45 (0.37), residues: 158
  loop : -2.29 (0.21), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.002   ARG B 292 
 TYR   0.028   0.004   TYR A  64 
 PHE   0.023   0.003   PHE A 277 
 TRP   0.018   0.004   TRP A 575 
 HIS   0.011   0.003   HIS A 390 

Details of bonding type rmsd
  covalent geometry    : bond        0.00677 (12458)
  covalent geometry    : angle       1.05823 (16884)
  SS BOND              : bond        0.01116 (   20)
  SS BOND              : angle       3.86419 (   40)
  hydrogen bonds       : bond        0.15203 (  612)
  hydrogen bonds       : angle       5.97469 ( 1776)
  link_NAG-ASN         : bond        0.01750 (    2)
  link_NAG-ASN         : angle       8.60445 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 223
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8471 (ttt)
REVERT: A  375 SER cc_start: 0.7607 (p) cc_final: 0.7096 (t)
REVERT: A  472 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8816 (mttp)
REVERT: A  668 ARG cc_start: 0.7222 (ptm160) cc_final: 0.6766 (mtm110)
REVERT: A  825 ILE cc_start: 0.7842 (mm) cc_final: 0.7431 (mm)
REVERT: B  513 GLU cc_start: 0.8281 (pm20) cc_final: 0.7758 (mm-30)
REVERT: B  618 CYS cc_start: 0.7836 (m) cc_final: 0.6285 (t)
  outliers start: 20
  outliers final: 3
  residues processed: 235
  average time/residue: 0.1111
  time to fit residues: 37.8655
Evaluate side-chains
  179 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 175
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue  755 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0170
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    2.5822

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

Flipped N/Q/H residues before XYZ refinement:
A 704 GLN
B  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.150491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.116103 restraints weight = 17256.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.117100 restraints weight = 15019.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.118629 restraints weight = 11356.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.118703 restraints weight = 8958.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.118935 restraints weight = 8494.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12480  Z= 0.177
  Angle     :  0.650   9.071  16930  Z= 0.329
  Chirality :  0.046   0.259   1892
  Planarity :  0.004   0.044   2124
  Dihedral  :  8.626  93.766   1762
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.25 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.44 %
    Favored  : 83.84 %
  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 (0.21), residues: 1524
  helix:  1.20 (0.19), residues: 709
  sheet: -1.02 (0.39), residues: 155
  loop : -2.01 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 727 
 TYR   0.016   0.001   TYR A 792 
 PHE   0.018   0.002   PHE B 818 
 TRP   0.014   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12458)
  covalent geometry    : angle       0.64015 (16884)
  SS BOND              : bond        0.00442 (   20)
  SS BOND              : angle       1.62680 (   40)
  hydrogen bonds       : bond        0.05231 (  612)
  hydrogen bonds       : angle       4.58389 ( 1776)
  link_NAG-ASN         : bond        0.00844 (    2)
  link_NAG-ASN         : angle       4.63255 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 GLN cc_start: 0.7184 (mt0) cc_final: 0.6151 (mt0)
REVERT: A  360 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.6681 (mp-120)
REVERT: A  375 SER cc_start: 0.7621 (p) cc_final: 0.7155 (t)
REVERT: A  668 ARG cc_start: 0.7029 (ptm160) cc_final: 0.6757 (mtm110)
REVERT: A  744 LEU cc_start: 0.7996 (mm) cc_final: 0.7710 (pp)
REVERT: A  778 MET cc_start: 0.7403 (mmm) cc_final: 0.7152 (mmm)
REVERT: B  618 CYS cc_start: 0.6707 (m) cc_final: 0.6111 (t)
REVERT: B  627 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7570 (pp)
REVERT: B  778 MET cc_start: 0.7934 (mmm) cc_final: 0.7492 (mmm)
  outliers start: 36
  outliers final: 14
  residues processed: 225
  average time/residue: 0.1060
  time to fit residues: 35.1686
Evaluate side-chains
  187 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  416 MET
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  627 LEU
Chi-restraints excluded: chain B residue  651 ILE
Chi-restraints excluded: chain B residue  700 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 140 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN
B 641 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.159556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126559 restraints weight = 17282.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126412 restraints weight = 15597.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.128292 restraints weight = 14223.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.128458 restraints weight = 9718.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.128922 restraints weight = 9139.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12480  Z= 0.124
  Angle     :  0.605   9.448  16930  Z= 0.301
  Chirality :  0.044   0.256   1892
  Planarity :  0.003   0.045   2124
  Dihedral  :  7.617  91.076   1756
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.03 %
    Favored  : 81.57 %
  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: -0.31 (0.21), residues: 1524
  helix:  1.41 (0.19), residues: 714
  sheet: -0.91 (0.40), residues: 155
  loop : -1.92 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 727 
 TYR   0.019   0.001   TYR A 604 
 PHE   0.015   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12458)
  covalent geometry    : angle       0.59883 (16884)
  SS BOND              : bond        0.00303 (   20)
  SS BOND              : angle       1.25166 (   40)
  hydrogen bonds       : bond        0.04595 (  612)
  hydrogen bonds       : angle       4.42845 ( 1776)
  link_NAG-ASN         : bond        0.00816 (    2)
  link_NAG-ASN         : angle       3.73185 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 179
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 SER cc_start: 0.7465 (p) cc_final: 0.7078 (t)
REVERT: A  568 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6331 (tp)
REVERT: A  744 LEU cc_start: 0.7986 (mm) cc_final: 0.7740 (pp)
REVERT: B  618 CYS cc_start: 0.6305 (m) cc_final: 0.5999 (t)
  outliers start: 45
  outliers final: 21
  residues processed: 210
  average time/residue: 0.1003
  time to fit residues: 31.3697
Evaluate side-chains
  191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  719 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 66 optimal weight:    0.0870
   chunk 41 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 125 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 130 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   overall best weight:    2.4166

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.159229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.125823 restraints weight = 16995.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.124813 restraints weight = 16600.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126692 restraints weight = 12922.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.126927 restraints weight = 9786.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.127303 restraints weight = 8924.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.491  12480  Z= 0.263
  Angle     :  0.645  20.883  16930  Z= 0.319
  Chirality :  0.044   0.256   1892
  Planarity :  0.003   0.045   2124
  Dihedral  :  7.619  91.076   1756
  Min Nonbonded Distance : 1.561

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.99 %
    Favored  : 81.34 %
  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: -0.31 (0.21), residues: 1524
  helix:  1.41 (0.19), residues: 714
  sheet: -0.91 (0.40), residues: 155
  loop : -1.92 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 727 
 TYR   0.019   0.001   TYR A 604 
 PHE   0.015   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12458)
  covalent geometry    : angle       0.60000 (16884)
  SS BOND              : bond        0.11495 (   20)
  SS BOND              : angle       4.66734 (   40)
  hydrogen bonds       : bond        0.04595 (  612)
  hydrogen bonds       : angle       4.42845 ( 1776)
  link_NAG-ASN         : bond        0.00816 (    2)
  link_NAG-ASN         : angle       3.73186 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 SER cc_start: 0.7515 (p) cc_final: 0.7089 (t)
REVERT: A  568 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6343 (tp)
REVERT: A  744 LEU cc_start: 0.8020 (mm) cc_final: 0.7755 (pp)
REVERT: B  618 CYS cc_start: 0.6408 (m) cc_final: 0.6021 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 185
  average time/residue: 0.1027
  time to fit residues: 28.4235
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  719 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 138 optimal weight:    5.9990
   chunk 143 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0570
   chunk 81 optimal weight:    3.9990
   chunk 118 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    3.2106

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.159170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125839 restraints weight = 17127.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.124133 restraints weight = 15545.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.125598 restraints weight = 13033.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.126298 restraints weight = 10021.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.126732 restraints weight = 8727.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.490  12480  Z= 0.263
  Angle     :  0.645  20.876  16930  Z= 0.319
  Chirality :  0.044   0.256   1892
  Planarity :  0.003   0.045   2124
  Dihedral  :  7.636  91.077   1756
  Min Nonbonded Distance : 1.562

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.07 %
    Favored  : 81.27 %
  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: -0.31 (0.21), residues: 1524
  helix:  1.41 (0.19), residues: 714
  sheet: -0.91 (0.40), residues: 155
  loop : -1.92 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 727 
 TYR   0.019   0.001   TYR A 604 
 PHE   0.015   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12458)
  covalent geometry    : angle       0.59999 (16884)
  SS BOND              : bond        0.11486 (   20)
  SS BOND              : angle       4.66567 (   40)
  hydrogen bonds       : bond        0.04595 (  612)
  hydrogen bonds       : angle       4.42845 ( 1776)
  link_NAG-ASN         : bond        0.00816 (    2)
  link_NAG-ASN         : angle       3.73186 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 SER cc_start: 0.7533 (p) cc_final: 0.7092 (t)
REVERT: A  568 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6352 (tp)
REVERT: A  744 LEU cc_start: 0.8091 (mm) cc_final: 0.7779 (pp)
REVERT: B  618 CYS cc_start: 0.6571 (m) cc_final: 0.6081 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 184
  average time/residue: 0.1015
  time to fit residues: 28.0675
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  719 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 146 optimal weight:    0.0570
   chunk 82 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   chunk 131 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 139 optimal weight:   20.0000
   overall best weight:    1.1704

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.159280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.125750 restraints weight = 17105.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124936 restraints weight = 16569.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126777 restraints weight = 12943.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.127010 restraints weight = 9608.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.127336 restraints weight = 8821.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.484  12480  Z= 0.260
  Angle     :  0.644  20.752  16930  Z= 0.318
  Chirality :  0.044   0.256   1892
  Planarity :  0.003   0.045   2124
  Dihedral  :  7.665  91.076   1756
  Min Nonbonded Distance : 1.570

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.07 %
    Favored  : 81.27 %
  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: -0.31 (0.21), residues: 1524
  helix:  1.41 (0.19), residues: 714
  sheet: -0.91 (0.40), residues: 155
  loop : -1.92 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 727 
 TYR   0.019   0.001   TYR A 604 
 PHE   0.015   0.001   PHE A 337 
 TRP   0.011   0.001   TRP A 336 
 HIS   0.003   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12458)
  covalent geometry    : angle       0.59987 (16884)
  SS BOND              : bond        0.11335 (   20)
  SS BOND              : angle       4.63781 (   40)
  hydrogen bonds       : bond        0.04595 (  612)
  hydrogen bonds       : angle       4.42845 ( 1776)
  link_NAG-ASN         : bond        0.00816 (    2)
  link_NAG-ASN         : angle       3.73189 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 SER cc_start: 0.7509 (p) cc_final: 0.7087 (t)
REVERT: A  568 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6343 (tp)
REVERT: A  744 LEU cc_start: 0.8013 (mm) cc_final: 0.7753 (pp)
REVERT: B  618 CYS cc_start: 0.6399 (m) cc_final: 0.6022 (t)
  outliers start: 22
  outliers final: 21
  residues processed: 184
  average time/residue: 0.1035
  time to fit residues: 28.9071
Evaluate side-chains
  190 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  719 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 105 optimal weight:    8.9990
   chunk 114 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 470 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.157940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124839 restraints weight = 17109.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.124454 restraints weight = 16046.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.126348 restraints weight = 14968.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.126512 restraints weight = 10130.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.127007 restraints weight = 9577.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12480  Z= 0.176
  Angle     :  0.648   9.809  16930  Z= 0.323
  Chirality :  0.045   0.252   1892
  Planarity :  0.004   0.044   2124
  Dihedral  :  7.273  88.701   1756
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.86 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.21), residues: 1524
  helix:  1.33 (0.19), residues: 707
  sheet: -0.89 (0.42), residues: 145
  loop : -1.92 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 727 
 TYR   0.016   0.001   TYR B 746 
 PHE   0.016   0.002   PHE A 337 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (12458)
  covalent geometry    : angle       0.64020 (16884)
  SS BOND              : bond        0.00337 (   20)
  SS BOND              : angle       1.58714 (   40)
  hydrogen bonds       : bond        0.04671 (  612)
  hydrogen bonds       : angle       4.44374 ( 1776)
  link_NAG-ASN         : bond        0.00608 (    2)
  link_NAG-ASN         : angle       3.73678 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 173
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.8471 (mtt) cc_final: 0.8097 (mtt)
REVERT: A  375 SER cc_start: 0.7471 (p) cc_final: 0.7036 (t)
REVERT: A  568 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6389 (tp)
REVERT: B  618 CYS cc_start: 0.6492 (m) cc_final: 0.6237 (t)
  outliers start: 45
  outliers final: 27
  residues processed: 204
  average time/residue: 0.0989
  time to fit residues: 30.2423
Evaluate side-chains
  195 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  736 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 144 optimal weight:    7.9990
   chunk 94 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 129 optimal weight:   10.0000
   chunk 117 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 150 optimal weight:    0.9980
   chunk 128 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
B  45 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.157424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.124407 restraints weight = 17123.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123773 restraints weight = 15574.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.125565 restraints weight = 15815.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.125747 restraints weight = 10088.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125931 restraints weight = 10939.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12480  Z= 0.197
  Angle     :  0.667   9.919  16930  Z= 0.329
  Chirality :  0.046   0.250   1892
  Planarity :  0.004   0.045   2124
  Dihedral  :  7.158  88.038   1756
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.92 %
    Favored  : 80.06 %
  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: -0.40 (0.21), residues: 1524
  helix:  1.30 (0.19), residues: 707
  sheet: -0.88 (0.42), residues: 145
  loop : -1.90 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 727 
 TYR   0.013   0.001   TYR B 746 
 PHE   0.017   0.002   PHE B 277 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12458)
  covalent geometry    : angle       0.65958 (16884)
  SS BOND              : bond        0.00337 (   20)
  SS BOND              : angle       1.55319 (   40)
  hydrogen bonds       : bond        0.04715 (  612)
  hydrogen bonds       : angle       4.44056 ( 1776)
  link_NAG-ASN         : bond        0.00577 (    2)
  link_NAG-ASN         : angle       3.68676 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.8463 (mtt) cc_final: 0.8063 (mtt)
REVERT: A  375 SER cc_start: 0.7491 (p) cc_final: 0.7048 (t)
REVERT: A  568 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6391 (tp)
REVERT: B  618 CYS cc_start: 0.6593 (m) cc_final: 0.6299 (t)
  outliers start: 40
  outliers final: 32
  residues processed: 198
  average time/residue: 0.0933
  time to fit residues: 27.9982
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  277 PHE
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  277 PHE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  736 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 105 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0170
   chunk 13 optimal weight:    0.7980
   chunk 86 optimal weight:    6.9990
   chunk 127 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   overall best weight:    1.1422

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.157488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124198 restraints weight = 17152.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.123751 restraints weight = 15560.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125209 restraints weight = 16573.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125390 restraints weight = 10651.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.125853 restraints weight = 9591.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12480  Z= 0.197
  Angle     :  0.667   9.919  16930  Z= 0.329
  Chirality :  0.046   0.250   1892
  Planarity :  0.004   0.045   2124
  Dihedral  :  7.170  88.038   1756
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.22 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.21), residues: 1524
  helix:  1.30 (0.19), residues: 707
  sheet: -0.88 (0.42), residues: 145
  loop : -1.90 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 727 
 TYR   0.013   0.001   TYR B 746 
 PHE   0.017   0.002   PHE B 277 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12458)
  covalent geometry    : angle       0.65973 (16884)
  SS BOND              : bond        0.00337 (   20)
  SS BOND              : angle       1.55293 (   40)
  hydrogen bonds       : bond        0.04715 (  612)
  hydrogen bonds       : angle       4.44057 ( 1776)
  link_NAG-ASN         : bond        0.00577 (    2)
  link_NAG-ASN         : angle       3.68676 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.8449 (mtt) cc_final: 0.8040 (mtt)
REVERT: A  375 SER cc_start: 0.7479 (p) cc_final: 0.7035 (t)
REVERT: A  568 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6400 (tp)
REVERT: B  618 CYS cc_start: 0.6564 (m) cc_final: 0.6287 (t)
  outliers start: 33
  outliers final: 32
  residues processed: 194
  average time/residue: 0.0989
  time to fit residues: 29.3236
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  277 PHE
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  277 PHE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  736 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 101 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 129 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0570
   chunk 2 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.0102

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.157490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124196 restraints weight = 17192.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.123778 restraints weight = 15534.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.125228 restraints weight = 16482.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125422 restraints weight = 10530.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.125899 restraints weight = 9522.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12480  Z= 0.197
  Angle     :  0.666   9.919  16930  Z= 0.329
  Chirality :  0.046   0.250   1892
  Planarity :  0.004   0.045   2124
  Dihedral  :  7.196  88.037   1756
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.22 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.21), residues: 1524
  helix:  1.30 (0.19), residues: 707
  sheet: -0.88 (0.42), residues: 145
  loop : -1.90 (0.22), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 727 
 TYR   0.013   0.001   TYR B 746 
 PHE   0.017   0.002   PHE B 277 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.004   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12458)
  covalent geometry    : angle       0.65935 (16884)
  SS BOND              : bond        0.00337 (   20)
  SS BOND              : angle       1.55162 (   40)
  hydrogen bonds       : bond        0.04714 (  612)
  hydrogen bonds       : angle       4.44058 ( 1776)
  link_NAG-ASN         : bond        0.00577 (    2)
  link_NAG-ASN         : angle       3.68681 (    6)

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

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

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3048 Ramachandran restraints generated.
    1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 MET cc_start: 0.8471 (mtt) cc_final: 0.8060 (mtt)
REVERT: A  375 SER cc_start: 0.7469 (p) cc_final: 0.7035 (t)
REVERT: A  568 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6387 (tp)
REVERT: B  618 CYS cc_start: 0.6499 (m) cc_final: 0.6263 (t)
  outliers start: 33
  outliers final: 32
  residues processed: 194
  average time/residue: 0.1007
  time to fit residues: 29.7773
Evaluate side-chains
  203 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  212 THR
Chi-restraints excluded: chain A residue  277 PHE
Chi-restraints excluded: chain A residue  417 SER
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  444 THR
Chi-restraints excluded: chain A residue  499 VAL
Chi-restraints excluded: chain A residue  502 LYS
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   57 CYS
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  277 PHE
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  499 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  530 CYS
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  636 ILE
Chi-restraints excluded: chain B residue  664 THR
Chi-restraints excluded: chain B residue  719 ILE
Chi-restraints excluded: chain B residue  736 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 117 optimal weight:    8.9990
   chunk 149 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0670
   chunk 24 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   overall best weight:    2.0126

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.158212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125514 restraints weight = 17111.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.125596 restraints weight = 13999.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.127145 restraints weight = 14361.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.127149 restraints weight = 9582.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.127635 restraints weight = 9929.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12480  Z= 0.157
  Angle     :  0.648  10.147  16930  Z= 0.320
  Chirality :  0.045   0.245   1892
  Planarity :  0.004   0.045   2124
  Dihedral  :  6.976  86.304   1756
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.84 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.21), residues: 1524
  helix:  1.26 (0.19), residues: 714
  sheet: -0.91 (0.42), residues: 145
  loop : -1.85 (0.22), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 668 
 TYR   0.022   0.001   TYR B 746 
 PHE   0.018   0.001   PHE B 818 
 TRP   0.012   0.001   TRP A 336 
 HIS   0.003   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12458)
  covalent geometry    : angle       0.64148 (16884)
  SS BOND              : bond        0.00318 (   20)
  SS BOND              : angle       1.45837 (   40)
  hydrogen bonds       : bond        0.04563 (  612)
  hydrogen bonds       : angle       4.39516 ( 1776)
  link_NAG-ASN         : bond        0.00574 (    2)
  link_NAG-ASN         : angle       3.68417 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1781.80 seconds
wall clock time: 31 minutes 46.14 seconds (1906.14 seconds total)