Starting phenix.real_space_refine
on Wed Mar  4 14:48:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t0u_10359/03_2026/6t0u_10359.map"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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
     P      23      5.49       5
     S      93      5.16       5
     C    8863      2.51       5
     N    2477      2.21       5
     O    2720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14176
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5741
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 704, 5733
          Classifications: {'peptide': 704}
          Link IDs: {'PTRANS': 25, 'TRANS': 678}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 704, 5733
          Classifications: {'peptide': 704}
          Link IDs: {'PTRANS': 25, 'TRANS': 678}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5846
    Chain: "B"
      Number of atoms: 5923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 5923
          Classifications: {'peptide': 740}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2020
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2020
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 12, 'TRANS': 238}
    Chain: "V"
      Number of atoms: 492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 492
          Classifications: {'RNA': 23}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 11, 'rna3p': 11}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AMET A 455 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CE BMET A 455 " occ=0.50
  Time building chain proxies: 3.83, per 1000 atoms: 0.27
  Number of scatterers: 14176
  At special positions: 0
  Unit cell: (96.39, 115.83, 117.45, 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      93     16.00
     P      23     15.00
     O    2720      8.00
     N    2477      7.00
     C    8863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 807.0 milliseconds
  

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3200

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 17 sheets defined
      51.0% alpha, 13.0% beta
      2 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
      removed outlier: 4.057A  pdb=" N   ASN A   8 " --> pdb=" O   PHE A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 25
      removed outlier: 3.637A  pdb=" N   TYR A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 50
    Processing helix  chain 'A' and resid 83 through 99
      removed outlier: 3.844A  pdb=" N   MET A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.561A  pdb=" N   TYR A 130 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 164 through 183
    Processing helix  chain 'A' and resid 187 through 193
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 240 through 249
      removed outlier: 3.618A  pdb=" N   ALA A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 330 through 346
      removed outlier: 3.913A  pdb=" N   TYR A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 366
    Processing helix  chain 'A' and resid 375 through 379
    Processing helix  chain 'A' and resid 400 through 410
      removed outlier: 3.625A  pdb=" N   SER A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER A 410 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 446
    Processing helix  chain 'A' and resid 448 through 471
      removed outlier: 3.714A  pdb=" N   GLU A 452 " --> pdb=" O   CYS A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 533
      removed outlier: 4.041A  pdb=" N   GLU A 533 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 575
      removed outlier: 3.549A  pdb=" N   GLU A 575 " --> pdb=" O   LYS A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 599
      removed outlier: 4.168A  pdb=" N   LEU A 580 " --> pdb=" O   MET A 576 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   ALA A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL A 597 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 609
      removed outlier: 3.856A  pdb=" N   ASN A 609 " --> pdb=" O   PRO A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 645
    Processing helix  chain 'A' and resid 647 through 669
      removed outlier: 3.685A  pdb=" N   GLU A 651 " --> pdb=" O   SER A 647 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   LYS A 659 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LEU A 660 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 689
      removed outlier: 3.560A  pdb=" N   LEU A 681 " --> pdb=" O   ASP A 677 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   CYS A 688 " --> pdb=" O   ALA A 684 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ILE A 689 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 712
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 14 through 22
      removed outlier: 3.793A  pdb=" N   ILE B  18 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   SER B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   THR B  20 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
    Processing helix  chain 'B' and resid 84 through 99
    Processing helix  chain 'B' and resid 101 through 115
      removed outlier: 3.520A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 124
      removed outlier: 3.537A  pdb=" N   LYS B 121 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 162 through 173
      removed outlier: 3.613A  pdb=" N   PHE B 166 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 176
      No H-bonds generated for 'chain 'B' and resid 174 through 176'
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 274 through 289
      removed outlier: 3.622A  pdb=" N   MET B 289 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 3.540A  pdb=" N   PHE B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR B 326 " --> pdb=" O   VAL B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 346
      removed outlier: 4.646A  pdb=" N   ALA B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 371 through 376
      removed outlier: 4.083A  pdb=" N   SER B 374 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE B 376 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 3.735A  pdb=" N   PHE B 381 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 414 through 427
      removed outlier: 4.230A  pdb=" N   GLY B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 433
      removed outlier: 3.643A  pdb=" N   LYS B 433 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 473
      removed outlier: 3.616A  pdb=" N   VAL B 473 " --> pdb=" O   THR B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 536
    Processing helix  chain 'B' and resid 540 through 559
    Processing helix  chain 'B' and resid 572 through 582
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.541A  pdb=" N   LEU B 589 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 613 through 616
      removed outlier: 3.661A  pdb=" N   MET B 616 " --> pdb=" O   TRP B 613 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 613 through 616'
    Processing helix  chain 'B' and resid 617 through 625
    Processing helix  chain 'B' and resid 683 through 700
      removed outlier: 3.876A  pdb=" N   ARG B 687 " --> pdb=" O   LEU B 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 732
      removed outlier: 3.537A  pdb=" N   ILE B 724 " --> pdb=" O   SER B 720 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 756
    Processing helix  chain 'C' and resid 0 through 13
      removed outlier: 3.612A  pdb=" N   ILE C   4 " --> pdb=" O   GLY C   0 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN C  13 " --> pdb=" O   GLU C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 23
    Processing helix  chain 'C' and resid 26 through 34
      removed outlier: 3.979A  pdb=" N   ILE C  31 " --> pdb=" O   MET C  28 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   LYS C  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR C  34 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 52
      removed outlier: 3.685A  pdb=" N   ALA C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 67
      removed outlier: 3.512A  pdb=" N   ILE C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 3.830A  pdb=" N   VAL C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.519A  pdb=" N   HIS C 127 " --> pdb=" O   GLU C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 168
      removed outlier: 3.743A  pdb=" N   GLN C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   GLU C 161 " --> pdb=" O   ARG C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 193
      removed outlier: 3.938A  pdb=" N   LEU C 183 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR C 184 " --> pdb=" O   ASP C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 225 through 230
      removed outlier: 3.554A  pdb=" N   VAL C 229 " --> pdb=" O   SER C 225 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLU C 230 " --> pdb=" O   SER C 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 225 through 230'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
      removed outlier: 3.682A  pdb=" N   PHE A  53 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275
      removed outlier: 6.365A  pdb=" N   LYS A 274 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293
      removed outlier: 7.058A  pdb=" N   TYR A 496 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ILE A 552 " --> pdb=" O   GLU A 544 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   GLU A 544 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   LYS A 554 " --> pdb=" O   ASP A 542 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ASP A 542 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL A 556 " --> pdb=" O   ILE A 540 " (cutoff:3.500A)
      removed outlier: 9.607A  pdb=" N   CYS A 536 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   ILE A 322 " --> pdb=" O   CYS A 536 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   LEU A 538 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   ALA A 320 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   ILE A 540 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293
      removed outlier: 5.378A  pdb=" N   THR A 493 " --> pdb=" O   CYS A 484 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   CYS A 484 " --> pdb=" O   THR A 493 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   LEU A 495 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   THR A 482 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   GLY A 497 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 373
      removed outlier: 5.877A  pdb=" N   GLU A 372 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   GLN B 367 " --> pdb=" O   GLU A 372 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626
      removed outlier: 6.543A  pdb=" N   GLY A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   GLU A 618 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLU A 624 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 183
    Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 193
      removed outlier: 3.778A  pdb=" N   LYS B 198 " --> pdb=" O   ASP B 193 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243
      removed outlier: 6.802A  pdb=" N   LEU B 224 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 492
    Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59
    Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 135
      removed outlier: 4.536A  pdb=" N   GLN C 243 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLU C 241 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148
      removed outlier: 6.658A  pdb=" N   ARG C 214 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)

    673 hydrogen bonds defined for protein.
    1864 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      5 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3932
        1.33 -     1.45: 2681
        1.45 -     1.57: 7691
        1.57 -     1.69: 44
        1.69 -     1.81: 162
  Bond restraints: 14510
  Sorted by residual:
  bond pdb=" CA  SER A 504 "
       pdb=" CB  SER A 504 "
    ideal  model  delta    sigma   weight residual
    1.531  1.488  0.043 3.12e-02 1.03e+03 1.88e+00
  bond pdb=" CB  VAL A 695 "
       pdb=" CG2 VAL A 695 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.58e+00
  bond pdb=" CG1 ILE C  67 "
       pdb=" CD1 ILE C  67 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.51e+00
  bond pdb=" C   GLU A 604 "
       pdb=" N   PRO A 605 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 1.28e-02 6.10e+03 1.47e+00
  bond pdb=" CA  ILE A 689 "
       pdb=" CB  ILE A 689 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.35e+00
  ... (remaining 14505 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 19459
        2.46 -     4.92: 193
        4.92 -     7.38: 17
        7.38 -     9.84: 1
        9.84 -    12.30: 1
  Bond angle restraints: 19671
  Sorted by residual:
  angle pdb=" CA  ARG B 734 "
        pdb=" C   ARG B 734 "
        pdb=" N   ILE B 735 "
      ideal   model   delta    sigma   weight residual
     116.84  124.94   -8.10 1.71e+00 3.42e-01 2.24e+01
  angle pdb=" C   GLY B 733 "
        pdb=" N   ARG B 734 "
        pdb=" CA  ARG B 734 "
      ideal   model   delta    sigma   weight residual
     121.54  128.69   -7.15 1.91e+00 2.74e-01 1.40e+01
  angle pdb=" CA  ARG B 734 "
        pdb=" C   ARG B 734 "
        pdb=" O   ARG B 734 "
      ideal   model   delta    sigma   weight residual
     120.51  115.35    5.16 1.43e+00 4.89e-01 1.30e+01
  angle pdb=" C   HIS A 297 "
        pdb=" N   GLU A 298 "
        pdb=" CA  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     121.54  128.19   -6.65 1.91e+00 2.74e-01 1.21e+01
  angle pdb=" N   ILE A 302 "
        pdb=" CA  ILE A 302 "
        pdb=" C   ILE A 302 "
      ideal   model   delta    sigma   weight residual
     108.95  105.69    3.26 9.80e-01 1.04e+00 1.11e+01
  ... (remaining 19666 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 7921
       17.36 -    34.71: 679
       34.71 -    52.07: 189
       52.07 -    69.42: 57
       69.42 -    86.78: 15
  Dihedral angle restraints: 8861
    sinusoidal: 3913
      harmonic: 4948
  Sorted by residual:
  dihedral pdb=" CA  GLY B 733 "
           pdb=" C   GLY B 733 "
           pdb=" N   ARG B 734 "
           pdb=" CA  ARG B 734 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.96  -25.04     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ILE A 481 "
           pdb=" C   ILE A 481 "
           pdb=" N   THR A 482 "
           pdb=" CA  THR A 482 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  LYS B 152 "
           pdb=" C   LYS B 152 "
           pdb=" N   ASN B 153 "
           pdb=" CA  ASN B 153 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.08   17.92     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 8858 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1397
       0.040 -    0.080: 589
       0.080 -    0.120: 137
       0.120 -    0.160: 30
       0.160 -    0.200: 6
  Chirality restraints: 2159
  Sorted by residual:
  chirality pdb=" C1'   A V   4 "
            pdb=" O4'   A V   4 "
            pdb=" C2'   A V   4 "
            pdb=" N9    A V   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.26    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CB  ILE A 402 "
            pdb=" CA  ILE A 402 "
            pdb=" CG1 ILE A 402 "
            pdb=" CG2 ILE A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CB  ILE B 484 "
            pdb=" CA  ILE B 484 "
            pdb=" CG1 ILE B 484 "
            pdb=" CG2 ILE B 484 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 2156 not shown)

  Planarity restraints: 2449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   7 "   -0.031 2.00e-02 2.50e+03   1.41e-02 5.48e+00
        pdb=" N9    A V   7 "    0.033 2.00e-02 2.50e+03
        pdb=" C8    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A V   7 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A V   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A V   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A V   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A V   7 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  27 "   -0.036 5.00e-02 4.00e+02   5.46e-02 4.78e+00
        pdb=" N   PRO A  28 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   4 "   -0.029 2.00e-02 2.50e+03   1.32e-02 4.77e+00
        pdb=" N9    A V   4 "    0.031 2.00e-02 2.50e+03
        pdb=" C8    A V   4 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   4 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A V   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A V   4 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1    A V   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A V   4 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   4 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    A V   4 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2446 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3766
        2.80 -     3.32: 11910
        3.32 -     3.85: 24212
        3.85 -     4.37: 29427
        4.37 -     4.90: 50140
  Nonbonded interactions: 119455
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B 522 "
            pdb=" OH  TYR B 559 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   ILE B 219 "
            pdb=" OG1 THR B 223 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ALA B 113 "
            pdb=" OG1 THR B 117 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OE1 GLU A 588 "
            pdb=" OG1 THR B 543 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   ALA B 659 "
            pdb=" OH  TYR C 111 "
     model   vdw
     2.297 3.040
  ... (remaining 119450 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     15.520
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
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      :  0.005   0.058  14510  Z= 0.233
  Angle     :  0.684  12.301  19671  Z= 0.391
  Chirality :  0.046   0.200   2159
  Planarity :  0.006   0.055   2449
  Dihedral  : 14.960  86.776   5661
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  :  8.91 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -3.41 (0.16), residues: 1686
  helix: -2.10 (0.14), residues: 773
  sheet: -1.77 (0.35), residues: 172
  loop : -2.45 (0.18), residues: 741

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  62 
 TYR   0.017   0.002   TYR B 557 
 PHE   0.021   0.002   PHE B 505 
 TRP   0.027   0.002   TRP C  49 
 HIS   0.006   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (14510)
  covalent geometry    : angle       0.68378 (19671)
  hydrogen bonds       : bond        0.15709 (  674)
  hydrogen bonds       : angle       6.97781 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 300
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LEU cc_start: 0.5435 (OUTLIER) cc_final: 0.5028 (mp)
REVERT: A   97 MET cc_start: 0.7774 (tmm) cc_final: 0.7551 (ttp)
REVERT: A  111 ASP cc_start: 0.7305 (t0) cc_final: 0.6711 (t0)
REVERT: A  142 ASN cc_start: 0.6742 (OUTLIER) cc_final: 0.5927 (t0)
REVERT: A  346 LYS cc_start: 0.8469 (tttt) cc_final: 0.8154 (mmtt)
REVERT: A  397 LYS cc_start: 0.8407 (tttt) cc_final: 0.8113 (ttmt)
REVERT: A  419 GLU cc_start: 0.7288 (tp30) cc_final: 0.7021 (mm-30)
REVERT: A  606 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7666 (m-80)
REVERT: B  191 ILE cc_start: 0.8341 (mt) cc_final: 0.7813 (pt)
REVERT: B  205 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (mp)
REVERT: B  353 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7361 (ptm160)
REVERT: B  368 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7868 (pt)
REVERT: B  554 ASP cc_start: 0.8241 (t70) cc_final: 0.8024 (t0)
REVERT: B  685 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7479 (t70)
REVERT: B  687 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6354 (ttp80)
REVERT: B  706 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7465 (mmm-85)
REVERT: B  742 GLU cc_start: 0.6890 (tp30) cc_final: 0.6347 (tt0)
REVERT: C    8 MET cc_start: 0.6869 (tmt) cc_final: 0.6644 (tpt)
REVERT: C   12 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6982 (mtmt)
REVERT: C   32 LYS cc_start: 0.7945 (tttt) cc_final: 0.7427 (tmtt)
REVERT: C  134 LYS cc_start: 0.8272 (mttt) cc_final: 0.7743 (mmmt)
REVERT: C  197 LYS cc_start: 0.6508 (mttt) cc_final: 0.6098 (mmtt)
REVERT: C  213 ARG cc_start: 0.7021 (ttt90) cc_final: 0.6643 (ttp80)
REVERT: C  215 THR cc_start: 0.7573 (p) cc_final: 0.7298 (p)
REVERT: C  220 ILE cc_start: 0.8552 (mm) cc_final: 0.8251 (mm)
  outliers start: 79
  outliers final: 28
  residues processed: 362
  average time/residue: 0.1364
  time to fit residues: 68.7441
Evaluate side-chains
  246 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 211
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 GLN
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  147 ILE
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  232 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 180 GLN
A 217 GLN
A 586 GLN
A 665 GLN
B  32 HIS
B  65 GLN
B 628 ASN
B 634 HIS
B 679 GLN
B 694 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 148 ASN
C 233 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.146842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.114557 restraints weight = 29680.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.12
r_work: 0.3019 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14510  Z= 0.138
  Angle     :  0.514   6.391  19671  Z= 0.276
  Chirality :  0.041   0.207   2159
  Planarity :  0.004   0.044   2449
  Dihedral  : 11.850  88.229   2258
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 12.23 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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 (0.19), residues: 1686
  helix: -0.04 (0.17), residues: 785
  sheet: -1.36 (0.38), residues: 167
  loop : -1.96 (0.20), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 135 
 TYR   0.020   0.001   TYR B 557 
 PHE   0.012   0.001   PHE B 333 
 TRP   0.025   0.001   TRP C  49 
 HIS   0.012   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (14510)
  covalent geometry    : angle       0.51399 (19671)
  hydrogen bonds       : bond        0.04011 (  674)
  hydrogen bonds       : angle       4.77689 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 226
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.5273 (mtt) cc_final: 0.5048 (ttm)
REVERT: A   42 MET cc_start: 0.7240 (mmm) cc_final: 0.7003 (mmm)
REVERT: A   55 ASP cc_start: 0.6592 (t0) cc_final: 0.6277 (t0)
REVERT: A   72 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4731 (mp)
REVERT: A   97 MET cc_start: 0.8067 (tmm) cc_final: 0.7784 (ttp)
REVERT: A  142 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.5823 (t0)
REVERT: A  155 MET cc_start: 0.4802 (mtt) cc_final: 0.4499 (mtp)
REVERT: A  346 LYS cc_start: 0.8909 (tttt) cc_final: 0.8232 (mmtt)
REVERT: A  381 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5998 (pp20)
REVERT: A  405 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8314 (mt-10)
REVERT: A  605 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8294 (Cg_endo)
REVERT: A  606 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7616 (m-80)
REVERT: A  713 MET cc_start: 0.8023 (mtm) cc_final: 0.7671 (ptp)
REVERT: B  191 ILE cc_start: 0.7993 (mt) cc_final: 0.7489 (pt)
REVERT: B  518 ASN cc_start: 0.8964 (p0) cc_final: 0.8619 (p0)
REVERT: B  687 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6278 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7673 (mmm-85)
REVERT: C    8 MET cc_start: 0.7263 (tmt) cc_final: 0.6898 (tpt)
REVERT: C   12 LYS cc_start: 0.7333 (mmtt) cc_final: 0.6972 (mtmt)
REVERT: C   32 LYS cc_start: 0.8288 (tttt) cc_final: 0.7478 (tmtt)
REVERT: C  134 LYS cc_start: 0.8434 (mttt) cc_final: 0.7732 (mmmt)
REVERT: C  148 ASN cc_start: 0.5919 (OUTLIER) cc_final: 0.5695 (t0)
REVERT: C  197 LYS cc_start: 0.6547 (mttt) cc_final: 0.5930 (mmtt)
REVERT: C  213 ARG cc_start: 0.7089 (ttt90) cc_final: 0.6424 (ttp80)
  outliers start: 52
  outliers final: 28
  residues processed: 262
  average time/residue: 0.1209
  time to fit residues: 45.6237
Evaluate side-chains
  226 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   59 ASN
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  117 MET
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  232 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 132 optimal weight:    8.9990
   chunk 129 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0770
   chunk 112 optimal weight:    4.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
B 186 GLN
B 628 ASN
B 694 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.117206 restraints weight = 23504.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.83
r_work: 0.3082 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14510  Z= 0.096
  Angle     :  0.467   9.210  19671  Z= 0.249
  Chirality :  0.039   0.189   2159
  Planarity :  0.003   0.040   2449
  Dihedral  : 11.316  87.156   2234
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.70 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.59 (0.20), residues: 1686
  helix:  0.91 (0.18), residues: 779
  sheet: -1.17 (0.38), residues: 179
  loop : -1.63 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  15 
 TYR   0.019   0.001   TYR A 144 
 PHE   0.021   0.001   PHE B 740 
 TRP   0.025   0.001   TRP C  49 
 HIS   0.009   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 (14510)
  covalent geometry    : angle       0.46664 (19671)
  hydrogen bonds       : bond        0.03404 (  674)
  hydrogen bonds       : angle       4.45024 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 218
  time to evaluate  : 0.513 
Fit side-chains
REVERT: A   55 ASP cc_start: 0.6609 (t0) cc_final: 0.6259 (t0)
REVERT: A   72 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4715 (mp)
REVERT: A   97 MET cc_start: 0.8028 (tmm) cc_final: 0.7684 (ttp)
REVERT: A  142 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.5637 (t0)
REVERT: A  155 MET cc_start: 0.4926 (mtt) cc_final: 0.4595 (mtp)
REVERT: A  346 LYS cc_start: 0.8851 (tttt) cc_final: 0.8202 (mmtt)
REVERT: A  405 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8281 (mt-10)
REVERT: A  606 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7473 (m-80)
REVERT: B  191 ILE cc_start: 0.7984 (mt) cc_final: 0.7567 (pt)
REVERT: B  353 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7679 (ptm160)
REVERT: B  429 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7016 (mtp180)
REVERT: B  518 ASN cc_start: 0.8900 (p0) cc_final: 0.8503 (p0)
REVERT: B  687 ARG cc_start: 0.7026 (mtt180) cc_final: 0.6268 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7579 (mmm-85)
REVERT: C    8 MET cc_start: 0.7344 (tmt) cc_final: 0.6929 (tpt)
REVERT: C   12 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7041 (mtmt)
REVERT: C   32 LYS cc_start: 0.8243 (tttt) cc_final: 0.7480 (tmtt)
REVERT: C  134 LYS cc_start: 0.8409 (mttt) cc_final: 0.7764 (mmmt)
REVERT: C  144 ARG cc_start: 0.7715 (ttt180) cc_final: 0.7506 (ttt180)
REVERT: C  197 LYS cc_start: 0.6538 (mttt) cc_final: 0.5921 (mmtt)
REVERT: C  213 ARG cc_start: 0.6889 (ttt90) cc_final: 0.6527 (ttp80)
  outliers start: 39
  outliers final: 22
  residues processed: 246
  average time/residue: 0.1202
  time to fit residues: 42.6182
Evaluate side-chains
  229 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 151 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0670
   chunk 147 optimal weight:    8.9990
   chunk 135 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.6126

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
B 628 ASN
B 694 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.145198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.114733 restraints weight = 24510.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.69
r_work: 0.3046 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2922
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2922 r_free = 0.2922    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2922
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14510  Z= 0.190
  Angle     :  0.529   6.818  19671  Z= 0.280
  Chirality :  0.042   0.214   2159
  Planarity :  0.004   0.041   2449
  Dihedral  : 11.222  90.374   2225
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.43 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.44 (0.20), residues: 1686
  helix:  1.11 (0.18), residues: 784
  sheet: -1.01 (0.38), residues: 174
  loop : -1.71 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 220 
 TYR   0.019   0.002   TYR B 557 
 PHE   0.019   0.002   PHE B 740 
 TRP   0.025   0.001   TRP C  49 
 HIS   0.007   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (14510)
  covalent geometry    : angle       0.52931 (19671)
  hydrogen bonds       : bond        0.03925 (  674)
  hydrogen bonds       : angle       4.50732 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 203
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.6578 (t0) cc_final: 0.6245 (t0)
REVERT: A   72 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4679 (mp)
REVERT: A   97 MET cc_start: 0.8024 (tmm) cc_final: 0.7752 (ttp)
REVERT: A  142 ASN cc_start: 0.6281 (OUTLIER) cc_final: 0.5577 (t0)
REVERT: A  155 MET cc_start: 0.4844 (mtt) cc_final: 0.4506 (mtp)
REVERT: A  346 LYS cc_start: 0.8803 (tttt) cc_final: 0.8182 (mmtt)
REVERT: A  351 LYS cc_start: 0.8819 (mttt) cc_final: 0.8460 (mtmt)
REVERT: A  405 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8342 (mt-10)
REVERT: B  112 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7401 (m-30)
REVERT: B  191 ILE cc_start: 0.7969 (mt) cc_final: 0.7493 (pt)
REVERT: B  429 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7070 (mtp180)
REVERT: B  518 ASN cc_start: 0.9027 (p0) cc_final: 0.8825 (p0)
REVERT: B  687 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6354 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7564 (mmm-85)
REVERT: C    8 MET cc_start: 0.7381 (tmt) cc_final: 0.6834 (tpt)
REVERT: C   12 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6975 (mttt)
REVERT: C   32 LYS cc_start: 0.8286 (tttt) cc_final: 0.7471 (tmtt)
REVERT: C  144 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7534 (ttt180)
REVERT: C  175 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5296 (mmp-170)
REVERT: C  197 LYS cc_start: 0.6617 (mttt) cc_final: 0.5983 (mmtt)
  outliers start: 49
  outliers final: 32
  residues processed: 235
  average time/residue: 0.1229
  time to fit residues: 41.0253
Evaluate side-chains
  230 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 18 optimal weight:   10.0000
   chunk 164 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 136 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 117 optimal weight:    0.3980
   chunk 55 optimal weight:    4.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:   30.0000
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.145349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.115961 restraints weight = 27373.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.67
r_work: 0.3066 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14510  Z= 0.153
  Angle     :  0.499   6.544  19671  Z= 0.265
  Chirality :  0.041   0.189   2159
  Planarity :  0.003   0.040   2449
  Dihedral  : 11.115  90.714   2221
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.03 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.17 (0.20), residues: 1686
  helix:  1.36 (0.19), residues: 779
  sheet: -0.94 (0.38), residues: 174
  loop : -1.56 (0.21), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 135 
 TYR   0.018   0.001   TYR B 557 
 PHE   0.019   0.001   PHE B 740 
 TRP   0.024   0.001   TRP C  49 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (14510)
  covalent geometry    : angle       0.49870 (19671)
  hydrogen bonds       : bond        0.03676 (  674)
  hydrogen bonds       : angle       4.41165 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 202
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.6628 (t0) cc_final: 0.6339 (t0)
REVERT: A   72 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4763 (mp)
REVERT: A   97 MET cc_start: 0.8015 (tmm) cc_final: 0.7753 (ttp)
REVERT: A  155 MET cc_start: 0.4814 (mtt) cc_final: 0.4522 (mtp)
REVERT: A  346 LYS cc_start: 0.8761 (tttt) cc_final: 0.8199 (mmtt)
REVERT: A  351 LYS cc_start: 0.8831 (mttt) cc_final: 0.8476 (mtmt)
REVERT: A  405 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8334 (mt-10)
REVERT: B  112 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7371 (m-30)
REVERT: B  191 ILE cc_start: 0.8007 (mt) cc_final: 0.7576 (pt)
REVERT: B  353 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7672 (ptm160)
REVERT: B  429 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7054 (mtp180)
REVERT: B  687 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6405 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7580 (mmm-85)
REVERT: C    8 MET cc_start: 0.7443 (tmt) cc_final: 0.7151 (tpt)
REVERT: C   12 LYS cc_start: 0.7438 (mmtt) cc_final: 0.7100 (mtmt)
REVERT: C   32 LYS cc_start: 0.8292 (tttt) cc_final: 0.7527 (tmtt)
REVERT: C  197 LYS cc_start: 0.6750 (mttt) cc_final: 0.6080 (mmtt)
  outliers start: 46
  outliers final: 35
  residues processed: 232
  average time/residue: 0.1250
  time to fit residues: 41.4574
Evaluate side-chains
  231 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 192
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  609 VAL
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 135 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 162 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 158 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 155 optimal weight:    0.7980
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.144837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.114408 restraints weight = 34185.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.18
r_work: 0.3014 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2876 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2876
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14510  Z= 0.161
  Angle     :  0.503   6.494  19671  Z= 0.267
  Chirality :  0.041   0.187   2159
  Planarity :  0.004   0.041   2449
  Dihedral  : 11.100  91.166   2219
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.23 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.08 (0.20), residues: 1686
  helix:  1.45 (0.18), residues: 781
  sheet: -0.86 (0.38), residues: 174
  loop : -1.55 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 135 
 TYR   0.018   0.001   TYR A 144 
 PHE   0.019   0.001   PHE B 740 
 TRP   0.022   0.001   TRP C  49 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (14510)
  covalent geometry    : angle       0.50292 (19671)
  hydrogen bonds       : bond        0.03719 (  674)
  hydrogen bonds       : angle       4.39698 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 197
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.8027 (tmm) cc_final: 0.7750 (ttp)
REVERT: A  155 MET cc_start: 0.4759 (mtt) cc_final: 0.4467 (mtp)
REVERT: A  346 LYS cc_start: 0.8794 (tttt) cc_final: 0.8194 (mmtt)
REVERT: A  351 LYS cc_start: 0.8848 (mttt) cc_final: 0.8490 (mtmt)
REVERT: A  405 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8406 (mt-10)
REVERT: B  112 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (m-30)
REVERT: B  191 ILE cc_start: 0.8031 (mt) cc_final: 0.7596 (pt)
REVERT: B  413 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7875 (t0)
REVERT: B  429 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7053 (mtp180)
REVERT: B  445 ASP cc_start: 0.8083 (p0) cc_final: 0.7862 (p0)
REVERT: B  687 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6409 (ttp-110)
REVERT: B  706 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7632 (mmm-85)
REVERT: C    8 MET cc_start: 0.7507 (tmt) cc_final: 0.7197 (tpt)
REVERT: C   12 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7064 (mtmt)
REVERT: C   32 LYS cc_start: 0.8352 (tttt) cc_final: 0.7557 (tmtt)
REVERT: C  134 LYS cc_start: 0.8326 (mttt) cc_final: 0.7714 (mmmt)
REVERT: C  175 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.5345 (mmp-170)
REVERT: C  197 LYS cc_start: 0.6780 (mttt) cc_final: 0.6154 (mmtt)
  outliers start: 50
  outliers final: 41
  residues processed: 229
  average time/residue: 0.1302
  time to fit residues: 42.3578
Evaluate side-chains
  236 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 191
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  713 MET
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  413 ASN
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  434 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  520 SER
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  609 VAL
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 124 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0170
   chunk 3 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1222

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.147156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.117870 restraints weight = 28748.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.71
r_work: 0.3082 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  14510  Z= 0.110
  Angle     :  0.467   6.619  19671  Z= 0.249
  Chirality :  0.039   0.175   2159
  Planarity :  0.003   0.038   2449
  Dihedral  : 10.887  89.243   2217
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.36 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.06 (0.20), residues: 1686
  helix:  1.57 (0.19), residues: 788
  sheet: -0.77 (0.40), residues: 167
  loop : -1.52 (0.21), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 135 
 TYR   0.019   0.001   TYR A 144 
 PHE   0.016   0.001   PHE C 168 
 TRP   0.027   0.001   TRP C  49 
 HIS   0.006   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (14510)
  covalent geometry    : angle       0.46724 (19671)
  hydrogen bonds       : bond        0.03330 (  674)
  hydrogen bonds       : angle       4.28318 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 205
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.6534 (t0) cc_final: 0.6235 (t0)
REVERT: A   72 LEU cc_start: 0.5300 (OUTLIER) cc_final: 0.5037 (mt)
REVERT: A   97 MET cc_start: 0.7973 (tmm) cc_final: 0.7731 (ttp)
REVERT: A  142 ASN cc_start: 0.6284 (OUTLIER) cc_final: 0.5552 (t0)
REVERT: A  155 MET cc_start: 0.4914 (mtt) cc_final: 0.4641 (mtp)
REVERT: A  346 LYS cc_start: 0.8746 (tttt) cc_final: 0.8200 (mmtt)
REVERT: A  351 LYS cc_start: 0.8819 (mttt) cc_final: 0.8503 (mtmt)
REVERT: B  112 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7450 (m-30)
REVERT: B  191 ILE cc_start: 0.7961 (mt) cc_final: 0.7561 (pt)
REVERT: B  353 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7774 (ttp-110)
REVERT: B  413 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7782 (t0)
REVERT: B  429 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7027 (mtp180)
REVERT: B  687 ARG cc_start: 0.7053 (mtt180) cc_final: 0.6387 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7586 (mmm-85)
REVERT: C    8 MET cc_start: 0.7456 (tmt) cc_final: 0.7161 (tpt)
REVERT: C   12 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7073 (mtmt)
REVERT: C   32 LYS cc_start: 0.8320 (tttt) cc_final: 0.7542 (tmtt)
REVERT: C   55 TYR cc_start: 0.8090 (m-80) cc_final: 0.7393 (m-80)
REVERT: C  134 LYS cc_start: 0.8337 (mttt) cc_final: 0.7738 (mmmt)
REVERT: C  175 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5365 (mmp-170)
REVERT: C  197 LYS cc_start: 0.6815 (mttt) cc_final: 0.6191 (mmtt)
  outliers start: 43
  outliers final: 30
  residues processed: 233
  average time/residue: 0.1263
  time to fit residues: 41.7681
Evaluate side-chains
  231 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 194
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  413 ASN
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 166 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 161 optimal weight:    0.0570
   chunk 60 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 147 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.3704

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

Flipped N/Q/H residues before XYZ refinement:
** C  13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.146754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117215 restraints weight = 27139.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.76
r_work: 0.3064 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2895
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2895 r_free = 0.2895    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2895
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14510  Z= 0.122
  Angle     :  0.475   6.581  19671  Z= 0.254
  Chirality :  0.040   0.171   2159
  Planarity :  0.003   0.039   2449
  Dihedral  : 10.774  89.380   2210
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.36 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.15 (0.20), residues: 1686
  helix:  1.62 (0.19), residues: 790
  sheet: -0.71 (0.40), residues: 167
  loop : -1.47 (0.21), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 135 
 TYR   0.018   0.001   TYR A 144 
 PHE   0.020   0.001   PHE B 740 
 TRP   0.028   0.001   TRP C  98 
 HIS   0.005   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (14510)
  covalent geometry    : angle       0.47547 (19671)
  hydrogen bonds       : bond        0.03406 (  674)
  hydrogen bonds       : angle       4.26115 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.6473 (t0) cc_final: 0.6152 (t0)
REVERT: A   72 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4956 (mt)
REVERT: A   97 MET cc_start: 0.8002 (tmm) cc_final: 0.7752 (ttp)
REVERT: A  142 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5547 (t0)
REVERT: A  155 MET cc_start: 0.4825 (mtt) cc_final: 0.4564 (mtp)
REVERT: A  346 LYS cc_start: 0.8768 (tttt) cc_final: 0.8172 (mmtt)
REVERT: A  351 LYS cc_start: 0.8836 (mttt) cc_final: 0.8505 (mtmt)
REVERT: B  112 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7612 (m-30)
REVERT: B  191 ILE cc_start: 0.7907 (mt) cc_final: 0.7446 (pt)
REVERT: B  199 MET cc_start: 0.8337 (mmm) cc_final: 0.8032 (mmm)
REVERT: B  353 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7740 (ttp-110)
REVERT: B  413 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7816 (t0)
REVERT: B  429 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7070 (mtp180)
REVERT: B  687 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6300 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7517 (mmm-85)
REVERT: C    8 MET cc_start: 0.7444 (tmt) cc_final: 0.7148 (tpt)
REVERT: C   12 LYS cc_start: 0.7415 (mmtt) cc_final: 0.7078 (mtmt)
REVERT: C   32 LYS cc_start: 0.8321 (tttt) cc_final: 0.7322 (tptp)
REVERT: C   55 TYR cc_start: 0.8083 (m-80) cc_final: 0.7371 (m-80)
REVERT: C  134 LYS cc_start: 0.8323 (mttt) cc_final: 0.7658 (mmmt)
REVERT: C  175 ARG cc_start: 0.6635 (OUTLIER) cc_final: 0.5414 (mmp-170)
REVERT: C  197 LYS cc_start: 0.6823 (mttt) cc_final: 0.6173 (mmtt)
  outliers start: 44
  outliers final: 30
  residues processed: 222
  average time/residue: 0.1313
  time to fit residues: 41.9229
Evaluate side-chains
  227 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  413 ASN
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  609 VAL
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 158 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 140 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   chunk 143 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 110 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 163 optimal weight:    6.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN
C  13 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.112803 restraints weight = 20008.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 1.44
r_work: 0.3079 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  14510  Z= 0.220
  Angle     :  0.549   7.556  19671  Z= 0.291
  Chirality :  0.043   0.208   2159
  Planarity :  0.004   0.042   2449
  Dihedral  : 10.953  92.497   2209
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.69 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.01 (0.20), residues: 1686
  helix:  1.46 (0.18), residues: 790
  sheet: -0.73 (0.39), residues: 174
  loop : -1.51 (0.21), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 135 
 TYR   0.018   0.002   TYR B 557 
 PHE   0.017   0.002   PHE A 515 
 TRP   0.034   0.002   TRP C  98 
 HIS   0.004   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 (14510)
  covalent geometry    : angle       0.54874 (19671)
  hydrogen bonds       : bond        0.04014 (  674)
  hydrogen bonds       : angle       4.42697 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 187
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 ASP cc_start: 0.6508 (t0) cc_final: 0.6256 (t0)
REVERT: A   72 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.5042 (mt)
REVERT: A   97 MET cc_start: 0.8015 (tmm) cc_final: 0.7725 (ttp)
REVERT: A  142 ASN cc_start: 0.6344 (OUTLIER) cc_final: 0.5617 (t0)
REVERT: A  155 MET cc_start: 0.4695 (mtt) cc_final: 0.4424 (mtp)
REVERT: A  346 LYS cc_start: 0.8732 (tttt) cc_final: 0.8150 (mmtt)
REVERT: A  351 LYS cc_start: 0.8834 (mttt) cc_final: 0.8465 (mtmt)
REVERT: B  112 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7582 (m-30)
REVERT: B  191 ILE cc_start: 0.7954 (mt) cc_final: 0.7521 (pt)
REVERT: B  353 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7397 (ptm160)
REVERT: B  413 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7798 (t0)
REVERT: B  429 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7028 (mtp180)
REVERT: B  687 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6336 (ttp-110)
REVERT: B  706 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7549 (mmm-85)
REVERT: C    8 MET cc_start: 0.7429 (tmt) cc_final: 0.7124 (tpt)
REVERT: C   12 LYS cc_start: 0.7398 (mmtt) cc_final: 0.7084 (mtmt)
REVERT: C   32 LYS cc_start: 0.8308 (tttt) cc_final: 0.7458 (tmtt)
REVERT: C  134 LYS cc_start: 0.8284 (mttt) cc_final: 0.7623 (mmmt)
REVERT: C  175 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5312 (mmp-170)
REVERT: C  197 LYS cc_start: 0.6866 (mttt) cc_final: 0.6230 (mmtt)
  outliers start: 45
  outliers final: 34
  residues processed: 219
  average time/residue: 0.1252
  time to fit residues: 39.4982
Evaluate side-chains
  225 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 184
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  285 MET
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  413 ASN
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  520 SER
Chi-restraints excluded: chain B residue  529 VAL
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  609 VAL
Chi-restraints excluded: chain B residue  628 ASN
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 169 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 28 optimal weight:    8.9990
   chunk 147 optimal weight:    0.9990
   chunk 140 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 665 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.142786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.112382 restraints weight = 34037.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.16
r_work: 0.2976 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8663
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  14510  Z= 0.235
  Angle     :  0.572   8.299  19671  Z= 0.303
  Chirality :  0.044   0.201   2159
  Planarity :  0.004   0.042   2449
  Dihedral  : 11.093  93.811   2209
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 17.09 %
    Favored  : 79.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.05 (0.20), residues: 1686
  helix:  1.40 (0.18), residues: 785
  sheet: -0.72 (0.39), residues: 174
  loop : -1.48 (0.21), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 135 
 TYR   0.017   0.002   TYR B 555 
 PHE   0.019   0.002   PHE A 515 
 TRP   0.029   0.002   TRP C  98 
 HIS   0.004   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (14510)
  covalent geometry    : angle       0.57152 (19671)
  hydrogen bonds       : bond        0.04178 (  674)
  hydrogen bonds       : angle       4.51792 ( 1874)

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

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

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3372 Ramachandran restraints generated.
    1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 183
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A   55 ASP cc_start: 0.6616 (t0) cc_final: 0.6337 (t0)
REVERT: A   72 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5146 (mt)
REVERT: A   97 MET cc_start: 0.8023 (tmm) cc_final: 0.7750 (ttp)
REVERT: A  142 ASN cc_start: 0.6231 (OUTLIER) cc_final: 0.5557 (t0)
REVERT: A  155 MET cc_start: 0.4849 (mtt) cc_final: 0.4519 (mtp)
REVERT: A  346 LYS cc_start: 0.8796 (tttt) cc_final: 0.8182 (mmtt)
REVERT: A  351 LYS cc_start: 0.8854 (mttt) cc_final: 0.8479 (mtmt)
REVERT: B  112 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7698 (m-30)
REVERT: B  191 ILE cc_start: 0.8047 (mt) cc_final: 0.7619 (pt)
REVERT: B  353 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7683 (ptm160)
REVERT: B  413 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.7914 (t0)
REVERT: B  429 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7041 (mtp180)
REVERT: B  687 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6420 (ttp-110)
REVERT: B  690 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7852 (mm110)
REVERT: C    8 MET cc_start: 0.7515 (tmt) cc_final: 0.7219 (tpt)
REVERT: C   12 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7150 (mtmt)
REVERT: C   32 LYS cc_start: 0.8433 (tttt) cc_final: 0.7585 (tmtt)
REVERT: C  134 LYS cc_start: 0.8327 (mttt) cc_final: 0.7678 (mmmt)
REVERT: C  175 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5314 (mmp-170)
REVERT: C  197 LYS cc_start: 0.7054 (mttt) cc_final: 0.6376 (mmtt)
  outliers start: 44
  outliers final: 33
  residues processed: 213
  average time/residue: 0.1297
  time to fit residues: 39.4189
Evaluate side-chains
  219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  224 LYS
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  286 ILE
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  314 ASN
Chi-restraints excluded: chain B residue  321 MET
Chi-restraints excluded: chain B residue  322 VAL
Chi-restraints excluded: chain B residue  353 ARG
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  413 ASN
Chi-restraints excluded: chain B residue  429 ARG
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  520 SER
Chi-restraints excluded: chain B residue  583 THR
Chi-restraints excluded: chain B residue  609 VAL
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  753 LEU
Chi-restraints excluded: chain C residue   28 MET
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  175 ARG
Chi-restraints excluded: chain C residue  179 SER
Chi-restraints excluded: chain C residue  203 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 171
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 99 optimal weight:    0.3980
   chunk 152 optimal weight:    9.9990
   chunk 6 optimal weight:    0.2980
   chunk 37 optimal weight:    4.9990
   chunk 163 optimal weight:    7.9990
   chunk 164 optimal weight:    0.0970
   chunk 156 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 461 ASN
A 505 HIS
C 138 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.118735 restraints weight = 33717.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.20
r_work: 0.3080 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2921
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2921 r_free = 0.2921    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2921
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14510  Z= 0.093
  Angle     :  0.475   6.916  19671  Z= 0.254
  Chirality :  0.039   0.171   2159
  Planarity :  0.003   0.037   2449
  Dihedral  : 10.788  88.584   2209
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.62 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.32 (0.21), residues: 1686
  helix:  1.73 (0.19), residues: 785
  sheet: -0.63 (0.41), residues: 167
  loop : -1.30 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 706 
 TYR   0.020   0.001   TYR A 144 
 PHE   0.022   0.001   PHE B 740 
 TRP   0.029   0.001   TRP C  98 
 HIS   0.005   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (14510)
  covalent geometry    : angle       0.47538 (19671)
  hydrogen bonds       : bond        0.03215 (  674)
  hydrogen bonds       : angle       4.26019 ( 1874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3913.90 seconds
wall clock time: 67 minutes 39.41 seconds (4059.41 seconds total)