Starting phenix.real_space_refine
on Thu Aug  6 10:34:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pnq_17783/08_2026/8pnq_17783.cif"
  }
  resolution = 2.88
  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=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P      50      5.49       5
     Mg      2      5.21       5
     S     104      5.16       5
     C    9214      2.51       5
     N    2587      2.21       5
     O    2956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14913
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 708, 5748
          Classifications: {'peptide': 708}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 675}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5958
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 744, 5950
          Classifications: {'peptide': 744}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 744, 5950
          Classifications: {'peptide': 744}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 713}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 6054
    Chain: "C"
      Number of atoms: 2024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2024
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
    Chain: "V"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 758
          Classifications: {'RNA': 36}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 9, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 13, 'rna3p': 22}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 202
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 9}
          Link IDs: {'rna3p': 8}
    Chain: "G"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 192
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 7, 'TRANS': 17}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 31
          Unusual residues: {' MG': 2, '2KH': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ALEU B 218 " occ=0.50
      ... (14 atoms not shown)
      pdb=" CD2BLEU B 218 " occ=0.50
  Time building chain proxies: 3.29, per 1000 atoms: 0.22
  Number of scatterers: 14913
  At special positions: 0
  Unit cell: (96.6, 100.8, 141.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S     104     16.00
     P      50     15.00
     Mg      2     11.99
     O    2956      8.00
     N    2587      7.00
     C    9214      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: 0.98
  Conformation dependent library (CDL) restraints added in 630.5 milliseconds
  

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3268

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 16 sheets defined
      52.0% alpha, 13.4% beta
      11 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 9
    Processing helix  chain 'A' and resid 10 through 23
    Processing helix  chain 'A' and resid 31 through 50
    Processing helix  chain 'A' and resid 83 through 99
    Processing helix  chain 'A' and resid 126 through 139
      removed outlier: 3.695A  pdb=" N   TYR A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 3.685A  pdb=" N   ARG A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 194
    Processing helix  chain 'A' and resid 195 through 198
    Processing helix  chain 'A' and resid 209 through 217
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 240 through 249
    Processing helix  chain 'A' and resid 302 through 313
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.586A  pdb=" N   TYR A 334 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 382 through 384
      No H-bonds generated for 'chain 'A' and resid 382 through 384'
    Processing helix  chain 'A' and resid 405 through 415
      removed outlier: 3.534A  pdb=" N   SER A 409 " --> pdb=" O   CYS A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 452
      removed outlier: 3.992A  pdb=" N   HIS A 452 " --> pdb=" O   ALA A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 476
    Processing helix  chain 'A' and resid 533 through 538
      removed outlier: 3.736A  pdb=" N   GLU A 538 " --> pdb=" O   HIS A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 580
    Processing helix  chain 'A' and resid 582 through 604
      removed outlier: 4.011A  pdb=" N   LEU A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLN A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL A 602 " --> pdb=" O   ALA A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 613
    Processing helix  chain 'A' and resid 632 through 650
    Processing helix  chain 'A' and resid 652 through 674
      removed outlier: 4.136A  pdb=" N   LYS A 664 " --> pdb=" O   ALA A 660 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   LEU A 665 " --> pdb=" O   GLU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 692
    Processing helix  chain 'A' and resid 697 through 716
      removed outlier: 3.950A  pdb=" N   ARG A 716 " --> pdb=" O   THR A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 14 through 22
      removed outlier: 5.447A  pdb=" N   SER B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE B  22 " --> pdb=" O   SER B  19 " (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 117
    Processing helix  chain 'B' and resid 118 through 125
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 160
    Processing helix  chain 'B' and resid 162 through 174
      removed outlier: 3.510A  pdb=" N   PHE B 166 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 222
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 3.567A  pdb=" N   ARG B 249 " --> pdb=" O   GLY B 245 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   GLY B 250 " --> pdb=" O   MET B 246 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LYS B 265 " --> pdb=" O   SER B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 293
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.522A  pdb=" N   ASN B 312 " --> pdb=" O   TRP B 309 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLN B 313 " --> pdb=" O   ASN B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 313'
    Processing helix  chain 'B' and resid 314 through 326
    Processing helix  chain 'B' and resid 330 through 346
      removed outlier: 4.685A  pdb=" N   ALA B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
      removed outlier: 3.597A  pdb=" N   ASN B 346 " --> pdb=" O   ILE B 342 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 376
      removed outlier: 4.205A  pdb=" N   ALA B 374 " --> pdb=" O   GLU B 371 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE B 376 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 412 through 426
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 455 through 474
    Processing helix  chain 'B' and resid 505 through 512
      Proline residue:  B 510  - end of helix
    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 583
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.829A  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 617 through 625
    Processing helix  chain 'B' and resid 679 through 700
      removed outlier: 3.782A  pdb=" N   GLU B 684 " --> pdb=" O   ARG B 680 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   ASP B 685 " --> pdb=" O   GLY B 681 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLU B 686 " --> pdb=" O   ILE B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 704
      removed outlier: 4.297A  pdb=" N   SER B 704 " --> pdb=" O   PRO B 701 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 701 through 704'
    Processing helix  chain 'B' and resid 713 through 733
    Processing helix  chain 'B' and resid 736 through 756
    Processing helix  chain 'C' and resid 2 through 13
      removed outlier: 3.827A  pdb=" N   GLN C  13 " --> pdb=" O   ASP C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 22
    Processing helix  chain 'C' and resid 24 through 33
      removed outlier: 4.194A  pdb=" N   ALA C  29 " --> pdb=" O   VAL C  25 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ILE C  30 " --> pdb=" O   ASP C  26 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LYS C  33 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 51
    Processing helix  chain 'C' and resid 62 through 67
      removed outlier: 3.689A  pdb=" N   MET C  66 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 3.742A  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
    Processing helix  chain 'C' and resid 155 through 168
    Processing helix  chain 'C' and resid 169 through 172
      removed outlier: 3.886A  pdb=" N   VAL C 172 " --> pdb=" O   PRO C 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 169 through 172'
    Processing helix  chain 'C' and resid 179 through 194
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 225 through 230
    Processing helix  chain 'C' and resid 231 through 236
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
      removed outlier: 3.758A  pdb=" N   LYS A  73 " --> pdb=" O   ILE A  54 " (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 290 through 293
      removed outlier: 7.404A  pdb=" N   TYR A 501 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   LEU A 549 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ARG A 559 " --> pdb=" O   ASP A 547 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ASP A 547 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   MET A 561 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   GLU A 544 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 322 " --> pdb=" O   GLU A 544 " (cutoff:3.500A)
      removed outlier: 8.784A  pdb=" N   GLY A 546 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 11.026A  pdb=" N   MET A 548 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 11.484A  pdb=" N   LYS A 318 " --> pdb=" O   MET A 548 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293
      removed outlier: 5.319A  pdb=" N   THR A 498 " --> pdb=" O   CYS A 489 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   CYS A 489 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   LEU A 500 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   SER A 487 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLY A 502 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   PHE A 480 " --> pdb=" O   MET A 360 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   LYS A 358 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 380
      removed outlier: 5.779A  pdb=" N   GLU A 377 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLN B 367 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   VAL A 379 " --> pdb=" O   GLN B 367 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631
      removed outlier: 6.268A  pdb=" N   GLY A 631 " --> pdb=" O   PRO A 620 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130
    Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181
    Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 192
      removed outlier: 8.061A  pdb=" N   SER B 678 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   ARG B 203 " --> pdb=" O   SER B 678 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 240 through 244
      removed outlier: 6.855A  pdb=" N   LEU B 224 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 492
    Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668
      removed outlier: 4.633A  pdb=" N   ILE B 667 " --> pdb=" O   THR C  58 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135
      removed outlier: 4.582A  pdb=" N   MET C 243 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   VAL C 133 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   GLU C 241 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 148
      removed outlier: 6.695A  pdb=" N   LYS C 214 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)

    723 hydrogen bonds defined for protein.
    2011 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 2.55

  Time building geometry restraints manager: 1.26 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 2393
        1.31 -     1.44: 4242
        1.44 -     1.57: 8393
        1.57 -     1.69: 101
        1.69 -     1.82: 180
  Bond restraints: 15309
  Sorted by residual:
  bond pdb=" N3A 2KH B 801 "
       pdb=" PA  2KH B 801 "
    ideal  model  delta    sigma   weight residual
    1.933  1.670  0.263 2.00e-02 2.50e+03 1.73e+02
  bond pdb=" C2' 2KH B 801 "
       pdb=" C3' 2KH B 801 "
    ideal  model  delta    sigma   weight residual
    1.548  1.310  0.238 2.00e-02 2.50e+03 1.42e+02
  bond pdb=" N3A 2KH B 801 "
       pdb=" PB  2KH B 801 "
    ideal  model  delta    sigma   weight residual
    1.890  1.697  0.193 2.00e-02 2.50e+03 9.33e+01
  bond pdb=" O3G 2KH B 801 "
       pdb=" PG  2KH B 801 "
    ideal  model  delta    sigma   weight residual
    1.669  1.497  0.172 2.00e-02 2.50e+03 7.39e+01
  bond pdb=" O2G 2KH B 801 "
       pdb=" PG  2KH B 801 "
    ideal  model  delta    sigma   weight residual
    1.682  1.528  0.154 2.00e-02 2.50e+03 5.91e+01
  ... (remaining 15304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    12.35: 20864
       12.35 -    24.70: 7
       24.70 -    37.05: 0
       37.05 -    49.40: 0
       49.40 -    61.75: 2
  Bond angle restraints: 20873
  Sorted by residual:
  angle pdb=" N3A 2KH B 801 "
        pdb=" PA  2KH B 801 "
        pdb=" O2A 2KH B 801 "
      ideal   model   delta    sigma   weight residual
      48.17  109.92  -61.75 3.00e+00 1.11e-01 4.24e+02
  angle pdb=" O2G 2KH B 801 "
        pdb=" PG  2KH B 801 "
        pdb=" O3G 2KH B 801 "
      ideal   model   delta    sigma   weight residual
      53.94  109.50  -55.56 3.00e+00 1.11e-01 3.43e+02
  angle pdb=" O1A 2KH B 801 "
        pdb=" PA  2KH B 801 "
        pdb=" O2A 2KH B 801 "
      ideal   model   delta    sigma   weight residual
     130.82  109.28   21.54 3.00e+00 1.11e-01 5.16e+01
  angle pdb=" O1G 2KH B 801 "
        pdb=" PG  2KH B 801 "
        pdb=" O2G 2KH B 801 "
      ideal   model   delta    sigma   weight residual
     130.21  109.42   20.79 3.00e+00 1.11e-01 4.80e+01
  angle pdb=" O1B 2KH B 801 "
        pdb=" PB  2KH B 801 "
        pdb=" O2B 2KH B 801 "
      ideal   model   delta    sigma   weight residual
     130.56  109.91   20.65 3.00e+00 1.11e-01 4.74e+01
  ... (remaining 20868 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.09: 8780
       32.09 -    64.18: 617
       64.18 -    96.26: 47
       96.26 -   128.35: 1
      128.35 -   160.44: 2
  Dihedral angle restraints: 9447
    sinusoidal: 4401
      harmonic: 5046
  Sorted by residual:
  dihedral pdb=" C5' 2KH B 801 "
           pdb=" O5' 2KH B 801 "
           pdb=" PA  2KH B 801 "
           pdb=" O2A 2KH B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      16.44 -144.00  160.44     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" O1A 2KH B 801 "
           pdb=" N3A 2KH B 801 "
           pdb=" PA  2KH B 801 "
           pdb=" PB  2KH B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     154.31  -46.11 -159.58     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C5' 2KH B 801 "
           pdb=" O5' 2KH B 801 "
           pdb=" PA  2KH B 801 "
           pdb=" O1A 2KH B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -149.66  -24.13 -125.53     1      3.00e+01 1.11e-03 1.69e+01
  ... (remaining 9444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 2162
       0.083 -    0.165: 150
       0.165 -    0.248: 2
       0.248 -    0.330: 0
       0.330 -    0.413: 1
  Chirality restraints: 2315
  Sorted by residual:
  chirality pdb=" C2' 2KH B 801 "
            pdb=" C1' 2KH B 801 "
            pdb=" C3' 2KH B 801 "
            pdb=" O2' 2KH B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.43   -0.41 2.00e-01 2.50e+01 4.26e+00
  chirality pdb=" C3' 2KH B 801 "
            pdb=" C2' 2KH B 801 "
            pdb=" C4' 2KH B 801 "
            pdb=" O3' 2KH B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.43   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" C1' 2KH B 801 "
            pdb=" C2' 2KH B 801 "
            pdb=" N1  2KH B 801 "
            pdb=" O4' 2KH B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.39    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2312 not shown)

  Planarity restraints: 2515
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 584 "    0.221 9.50e-02 1.11e+02   9.92e-02 6.73e+00
        pdb=" NE  ARG B 584 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 584 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 584 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 584 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   4 "   -0.024 2.00e-02 2.50e+03   1.04e-02 2.95e+00
        pdb=" N9    A V   4 "    0.023 2.00e-02 2.50e+03
        pdb=" C8    A V   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A V   4 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   4 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A V   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A V   4 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A V   4 "   -0.002 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
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   7 "   -0.020 2.00e-02 2.50e+03   9.34e-03 2.40e+00
        pdb=" N9    A V   7 "    0.022 2.00e-02 2.50e+03
        pdb=" C8    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A V   7 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    A V   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A V   7 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A V   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A V   7 "    0.002 2.00e-02 2.50e+03
  ... (remaining 2512 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.46: 64
        2.46 -     3.07: 10025
        3.07 -     3.68: 22963
        3.68 -     4.29: 35357
        4.29 -     4.90: 58414
  Nonbonded interactions: 126823
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 305 "
            pdb="MG    MG B 803 "
     model   vdw
     1.845 2.170
  nonbonded pdb=" OD2 ASP B 305 "
            pdb="MG    MG B 802 "
     model   vdw
     1.922 2.170
  nonbonded pdb=" O1B 2KH B 801 "
            pdb="MG    MG B 803 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" OG1 THR B 226 "
            pdb=" O   ARG B 350 "
     model   vdw
     2.054 3.040
  nonbonded pdb=" O1A 2KH B 801 "
            pdb="MG    MG B 803 "
     model   vdw
     2.084 2.170
  ... (remaining 126818 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:             3.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.070
  Find NCS groups from input model:        0.100
  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:8.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9027
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   0.263  15309  Z= 0.269
  Angle     :  0.843  61.746  20873  Z= 0.371
  Chirality :  0.039   0.413   2315
  Planarity :  0.003   0.099   2515
  Dihedral  : 19.332 160.439   6179
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 25.28 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.69 (0.21), residues: 1711
  helix:  2.41 (0.19), residues: 811
  sheet:  0.26 (0.36), residues: 193
  loop : -0.13 (0.23), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 584 
 TYR   0.014   0.001   TYR B 555 
 PHE   0.010   0.001   PHE A  53 
 TRP   0.014   0.001   TRP C  49 
 HIS   0.003   0.001   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00539 /  0.27 (15309)
  covalent geometry    : angle       0.84272 /  0.37 (20873)
  hydrogen bonds       : bond        0.12412 /  7.67 (  746)
  hydrogen bonds       : angle       5.28249 /  3.68 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6787 (mp0) cc_final: 0.6483 (pm20)
REVERT: A  168 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7139 (mtm110)
REVERT: A  201 ILE cc_start: 0.8780 (mm) cc_final: 0.8544 (mm)
REVERT: A  348 ILE cc_start: 0.8747 (tp) cc_final: 0.8476 (tp)
REVERT: C  243 MET cc_start: 0.8660 (mtp) cc_final: 0.8452 (mtp)
  outliers start: 30
  outliers final: 25
  residues processed: 218
  average time/residue: 0.5679
  time to fit residues: 136.1616
Evaluate side-chains
  206 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  405 CYS
Chi-restraints excluded: chain A residue  410 GLU
Chi-restraints excluded: chain A residue  499 ASN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  404 SER
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  506 SER
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  660 VAL
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain C residue  155 SER
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    7.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 124 GLN
B 158 ASN
B 184 HIS
C 100 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.105275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.075687 restraints weight = 49166.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.04
r_work: 0.2702 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9079
moved from start:          0.0770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15309  Z= 0.201
  Angle     :  0.549   8.886  20873  Z= 0.291
  Chirality :  0.042   0.167   2315
  Planarity :  0.004   0.044   2515
  Dihedral  : 13.531 135.067   2649
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.33 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.43 (0.20), residues: 1711
  helix:  2.06 (0.18), residues: 831
  sheet:  0.28 (0.36), residues: 196
  loop : -0.19 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 287 
 TYR   0.015   0.002   TYR B 557 
 PHE   0.012   0.001   PHE A 520 
 TRP   0.016   0.001   TRP C  49 
 HIS   0.007   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00467 /  0.20 (15309)
  covalent geometry    : angle       0.54933 /  0.29 (20873)
  hydrogen bonds       : bond        0.05011 /  3.29 (  746)
  hydrogen bonds       : angle       4.54894 /  3.17 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 200
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6589 (pm20)
REVERT: A  168 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7088 (mtm110)
REVERT: A  181 GLU cc_start: 0.7583 (tp30) cc_final: 0.7302 (tp30)
REVERT: A  191 PHE cc_start: 0.8230 (t80) cc_final: 0.7875 (t80)
REVERT: A  201 ILE cc_start: 0.8729 (mm) cc_final: 0.8507 (mm)
REVERT: A  348 ILE cc_start: 0.8697 (tp) cc_final: 0.8462 (tp)
REVERT: B    1 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6907 (tpp)
REVERT: B  566 THR cc_start: 0.8889 (OUTLIER) cc_final: 0.8636 (t)
REVERT: B  669 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7755 (ttmm)
REVERT: C   53 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7363 (mpt)
REVERT: G   11 SER cc_start: 0.4820 (OUTLIER) cc_final: 0.4490 (p)
  outliers start: 57
  outliers final: 21
  residues processed: 237
  average time/residue: 0.5346
  time to fit residues: 138.6682
Evaluate side-chains
  209 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  499 ASN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  637 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  669 LYS
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  117 THR
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 167 optimal weight:    0.0030
   chunk 131 optimal weight:    5.9990
   chunk 163 optimal weight:    2.9990
   chunk 140 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 156 optimal weight:    3.9990
   overall best weight:    1.3196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 116 GLN
B 124 GLN
B 158 ASN
C 100 ASN
C 182 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.106446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.078817 restraints weight = 27922.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.28
r_work: 0.2778 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9099
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15309  Z= 0.135
  Angle     :  0.491   9.055  20873  Z= 0.261
  Chirality :  0.039   0.178   2315
  Planarity :  0.004   0.040   2515
  Dihedral  : 13.344 135.895   2635
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 23.72 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.40 (0.20), residues: 1711
  helix:  2.04 (0.18), residues: 826
  sheet:  0.29 (0.36), residues: 196
  loop : -0.20 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 584 
 TYR   0.018   0.001   TYR B 557 
 PHE   0.009   0.001   PHE A 520 
 TRP   0.016   0.001   TRP C  49 
 HIS   0.004   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.13 (15309)
  covalent geometry    : angle       0.49071 /  0.26 (20873)
  hydrogen bonds       : bond        0.04370 /  2.90 (  746)
  hydrogen bonds       : angle       4.36381 /  3.04 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 202
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6540 (pm20)
REVERT: A   78 ILE cc_start: 0.8940 (mm) cc_final: 0.8674 (mm)
REVERT: A  168 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7094 (mtm110)
REVERT: A  181 GLU cc_start: 0.7626 (tp30) cc_final: 0.7254 (tp30)
REVERT: A  201 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8516 (mm)
REVERT: A  348 ILE cc_start: 0.8706 (tp) cc_final: 0.8466 (tp)
REVERT: A  551 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7660 (ttp80)
REVERT: B  208 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7628 (pttp)
REVERT: B  348 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8332 (mmm)
REVERT: B  566 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8642 (t)
REVERT: B  731 GLU cc_start: 0.8241 (tp30) cc_final: 0.7910 (mm-30)
REVERT: B  754 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7586 (ptt180)
REVERT: C   53 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7434 (mpt)
REVERT: C  192 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7564 (tm-30)
REVERT: G   20 THR cc_start: 0.9340 (m) cc_final: 0.9032 (p)
  outliers start: 56
  outliers final: 25
  residues processed: 237
  average time/residue: 0.5112
  time to fit residues: 132.6991
Evaluate side-chains
  219 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 186
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  499 ASN
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  637 ILE
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain B residue  754 ARG
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  192 GLU
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   18 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 154 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0030
   chunk 117 optimal weight:    4.9990
   chunk 102 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 149 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   overall best weight:    1.7196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 124 GLN
B 158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.105744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.076242 restraints weight = 49129.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.03
r_work: 0.2720 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2719
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2719 r_free = 0.2719    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2719
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9068
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  15309  Z= 0.150
  Angle     :  0.488   8.494  20873  Z= 0.260
  Chirality :  0.039   0.145   2315
  Planarity :  0.004   0.042   2515
  Dihedral  : 13.258 134.757   2631
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.20 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.25 (0.20), residues: 1711
  helix:  1.91 (0.18), residues: 838
  sheet:  0.25 (0.37), residues: 189
  loop : -0.32 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 584 
 TYR   0.019   0.001   TYR B 557 
 PHE   0.012   0.001   PHE B 185 
 TRP   0.017   0.001   TRP C  49 
 HIS   0.005   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 (15309)
  covalent geometry    : angle       0.48825 /  0.26 (20873)
  hydrogen bonds       : bond        0.04324 /  2.88 (  746)
  hydrogen bonds       : angle       4.30181 /  2.99 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 196
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6614 (pm20)
REVERT: A  147 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8200 (tt)
REVERT: A  168 ARG cc_start: 0.7606 (mtm-85) cc_final: 0.6962 (mtm110)
REVERT: A  181 GLU cc_start: 0.7711 (tp30) cc_final: 0.7006 (tp30)
REVERT: A  201 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (mm)
REVERT: A  348 ILE cc_start: 0.8698 (tp) cc_final: 0.8475 (tp)
REVERT: A  551 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7639 (ttp80)
REVERT: A  559 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8227 (mtm180)
REVERT: B    1 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6795 (tpp)
REVERT: B  174 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8900 (mtt)
REVERT: B  208 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7643 (pttp)
REVERT: B  348 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8259 (mmm)
REVERT: B  566 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8626 (t)
REVERT: B  731 GLU cc_start: 0.8215 (tp30) cc_final: 0.7891 (mm-30)
REVERT: C   53 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7276 (mpt)
REVERT: G   11 SER cc_start: 0.4738 (OUTLIER) cc_final: 0.4437 (p)
REVERT: G   20 THR cc_start: 0.9372 (m) cc_final: 0.9053 (p)
  outliers start: 68
  outliers final: 27
  residues processed: 240
  average time/residue: 0.5405
  time to fit residues: 142.0694
Evaluate side-chains
  228 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 190
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  512 ARG
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue   36 SER
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 159 optimal weight:    0.3980
   chunk 99 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 28 optimal weight:    5.9990
   chunk 166 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 116 GLN
B 134 ASN
B 158 ASN
C 100 ASN
C 233 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.078574 restraints weight = 37634.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.63
r_work: 0.2756 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9048
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15309  Z= 0.113
  Angle     :  0.478  11.357  20873  Z= 0.253
  Chirality :  0.038   0.148   2315
  Planarity :  0.003   0.041   2515
  Dihedral  : 13.161 133.278   2629
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.27 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.34 (0.20), residues: 1711
  helix:  1.99 (0.18), residues: 832
  sheet:  0.32 (0.37), residues: 189
  loop : -0.26 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 287 
 TYR   0.018   0.001   TYR B 557 
 PHE   0.009   0.001   PHE A 520 
 TRP   0.017   0.001   TRP C  49 
 HIS   0.003   0.001   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.11 (15309)
  covalent geometry    : angle       0.47837 /  0.25 (20873)
  hydrogen bonds       : bond        0.03954 /  2.64 (  746)
  hydrogen bonds       : angle       4.19590 /  2.91 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 202
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6527 (pm20)
REVERT: A  147 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: A  168 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7042 (mtm110)
REVERT: A  181 GLU cc_start: 0.7786 (tp30) cc_final: 0.7041 (tp30)
REVERT: A  195 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6334 (tm-30)
REVERT: A  201 ILE cc_start: 0.8743 (mm) cc_final: 0.8541 (mm)
REVERT: A  348 ILE cc_start: 0.8690 (tp) cc_final: 0.8473 (tp)
REVERT: A  559 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8197 (mtm180)
REVERT: B  208 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7697 (pttp)
REVERT: B  566 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (t)
REVERT: B  655 MET cc_start: 0.7226 (mmm) cc_final: 0.7001 (mmp)
REVERT: B  731 GLU cc_start: 0.8170 (tp30) cc_final: 0.7876 (mm-30)
REVERT: B  751 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8146 (tm-30)
REVERT: B  754 ARG cc_start: 0.8002 (ttt180) cc_final: 0.7552 (ptt180)
REVERT: C   53 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7236 (mpt)
REVERT: G   11 SER cc_start: 0.4709 (OUTLIER) cc_final: 0.4432 (p)
REVERT: G   20 THR cc_start: 0.9343 (m) cc_final: 0.9050 (p)
  outliers start: 62
  outliers final: 28
  residues processed: 246
  average time/residue: 0.5223
  time to fit residues: 141.0196
Evaluate side-chains
  225 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 189
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  603 LYS
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  640 VAL
Chi-restraints excluded: chain C residue    5 LYS
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 161 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 143 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 138 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0050
   overall best weight:    1.7800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 481 GLN
B 158 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.105583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.079223 restraints weight = 28687.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.02
r_work: 0.2775 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9102
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15309  Z= 0.153
  Angle     :  0.499   8.624  20873  Z= 0.264
  Chirality :  0.039   0.145   2315
  Planarity :  0.004   0.042   2515
  Dihedral  : 13.114 133.112   2628
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 23.40 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.25 (0.20), residues: 1711
  helix:  1.88 (0.18), residues: 839
  sheet:  0.40 (0.38), residues: 179
  loop : -0.31 (0.22), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 287 
 TYR   0.020   0.002   TYR A 130 
 PHE   0.015   0.001   PHE A  53 
 TRP   0.018   0.001   TRP C  49 
 HIS   0.005   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.15 (15309)
  covalent geometry    : angle       0.49913 /  0.26 (20873)
  hydrogen bonds       : bond        0.04240 /  2.83 (  746)
  hydrogen bonds       : angle       4.24033 /  2.95 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 199
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6543 (pm20)
REVERT: A  168 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7050 (mtm110)
REVERT: A  181 GLU cc_start: 0.7848 (tp30) cc_final: 0.7251 (tp30)
REVERT: A  191 PHE cc_start: 0.8292 (t80) cc_final: 0.8039 (t80)
REVERT: A  195 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6309 (tm-30)
REVERT: A  201 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8544 (mm)
REVERT: A  348 ILE cc_start: 0.8695 (tp) cc_final: 0.8476 (tp)
REVERT: A  551 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7688 (ttp80)
REVERT: B    1 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6845 (tpt)
REVERT: B  208 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7707 (pttp)
REVERT: B  566 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8610 (t)
REVERT: B  669 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7831 (ttmm)
REVERT: B  731 GLU cc_start: 0.8271 (tp30) cc_final: 0.7963 (mm-30)
REVERT: B  751 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: B  754 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7590 (ptt180)
REVERT: C   53 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7292 (mpt)
REVERT: C  146 ASP cc_start: 0.8508 (p0) cc_final: 0.8187 (p0)
REVERT: C  202 MET cc_start: 0.8480 (mtp) cc_final: 0.8255 (mmt)
REVERT: G   11 SER cc_start: 0.4720 (OUTLIER) cc_final: 0.4433 (p)
REVERT: G   20 THR cc_start: 0.9373 (m) cc_final: 0.9076 (p)
  outliers start: 62
  outliers final: 32
  residues processed: 238
  average time/residue: 0.5663
  time to fit residues: 147.6339
Evaluate side-chains
  233 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 191
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  603 LYS
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  208 LYS
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  633 SER
Chi-restraints excluded: chain B residue  669 LYS
Chi-restraints excluded: chain B residue  754 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 152 optimal weight:    9.9990
   chunk 83 optimal weight:    0.0050
   chunk 50 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 157 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 130 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 154 optimal weight:    0.9990
   overall best weight:    1.0198

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.078583 restraints weight = 41214.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.70
r_work: 0.2761 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9042
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  15309  Z= 0.112
  Angle     :  0.470   8.498  20873  Z= 0.250
  Chirality :  0.038   0.210   2315
  Planarity :  0.003   0.042   2515
  Dihedral  : 13.058 132.188   2627
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 24.04 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.32 (0.20), residues: 1711
  helix:  1.93 (0.18), residues: 833
  sheet:  0.45 (0.38), residues: 179
  loop : -0.27 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 287 
 TYR   0.020   0.001   TYR B 557 
 PHE   0.009   0.001   PHE A 520 
 TRP   0.019   0.001   TRP C  49 
 HIS   0.003   0.001   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 (15309)
  covalent geometry    : angle       0.47046 /  0.25 (20873)
  hydrogen bonds       : bond        0.03910 /  2.61 (  746)
  hydrogen bonds       : angle       4.16874 /  2.90 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 202
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6540 (pm20)
REVERT: A  134 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7891 (tptm)
REVERT: A  168 ARG cc_start: 0.7621 (mtm-85) cc_final: 0.6982 (mtm110)
REVERT: A  181 GLU cc_start: 0.7908 (tp30) cc_final: 0.7127 (tp30)
REVERT: A  201 ILE cc_start: 0.8748 (mm) cc_final: 0.8545 (mm)
REVERT: A  211 MET cc_start: 0.8823 (mmm) cc_final: 0.8623 (mmm)
REVERT: A  348 ILE cc_start: 0.8688 (tp) cc_final: 0.8473 (tp)
REVERT: B    1 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6747 (tpt)
REVERT: B  566 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8575 (t)
REVERT: B  731 GLU cc_start: 0.8240 (tp30) cc_final: 0.7945 (mm-30)
REVERT: B  751 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: B  754 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7582 (ptt180)
REVERT: C   53 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7135 (mpt)
REVERT: C  146 ASP cc_start: 0.8417 (p0) cc_final: 0.8080 (p0)
REVERT: G   11 SER cc_start: 0.4634 (OUTLIER) cc_final: 0.4363 (p)
REVERT: G   20 THR cc_start: 0.9314 (m) cc_final: 0.9048 (p)
  outliers start: 51
  outliers final: 28
  residues processed: 236
  average time/residue: 0.5867
  time to fit residues: 151.6482
Evaluate side-chains
  223 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 189
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  754 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Chi-restraints excluded: chain G residue   18 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 166 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0270
   chunk 44 optimal weight:    4.9990
   chunk 131 optimal weight:    0.4980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 582 GLN
C 236 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.108393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.080882 restraints weight = 30926.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.35
r_work: 0.2803 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  15309  Z= 0.097
  Angle     :  0.475  14.030  20873  Z= 0.249
  Chirality :  0.038   0.176   2315
  Planarity :  0.003   0.042   2515
  Dihedral  : 12.980 130.138   2627
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.56 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.35 (0.20), residues: 1711
  helix:  1.97 (0.18), residues: 834
  sheet:  0.42 (0.39), residues: 178
  loop : -0.26 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 287 
 TYR   0.018   0.001   TYR B 557 
 PHE   0.018   0.001   PHE A  53 
 TRP   0.018   0.001   TRP C  49 
 HIS   0.003   0.000   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00208 /  0.10 (15309)
  covalent geometry    : angle       0.47482 /  0.25 (20873)
  hydrogen bonds       : bond        0.03619 /  2.41 (  746)
  hydrogen bonds       : angle       4.10553 /  2.85 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 198
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6455 (pm20)
REVERT: A  134 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7899 (tptm)
REVERT: A  168 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7012 (mtm110)
REVERT: A  181 GLU cc_start: 0.7881 (tp30) cc_final: 0.7107 (tp30)
REVERT: A  201 ILE cc_start: 0.8789 (mm) cc_final: 0.8587 (mm)
REVERT: A  348 ILE cc_start: 0.8666 (tp) cc_final: 0.8438 (tp)
REVERT: A  543 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8981 (mt)
REVERT: B    1 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.6878 (tpt)
REVERT: B  566 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8599 (t)
REVERT: B  655 MET cc_start: 0.7211 (mmm) cc_final: 0.6980 (mmm)
REVERT: B  684 GLU cc_start: 0.7899 (tt0) cc_final: 0.7519 (tt0)
REVERT: B  731 GLU cc_start: 0.8295 (tp30) cc_final: 0.8014 (mm-30)
REVERT: B  751 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: B  754 ARG cc_start: 0.8000 (ttt180) cc_final: 0.7562 (ptt180)
REVERT: C   53 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7221 (mpt)
REVERT: C  146 ASP cc_start: 0.8545 (p0) cc_final: 0.8202 (p0)
REVERT: C  202 MET cc_start: 0.8457 (mtp) cc_final: 0.8246 (mmt)
REVERT: G   11 SER cc_start: 0.4665 (OUTLIER) cc_final: 0.4383 (p)
REVERT: G   20 THR cc_start: 0.9329 (m) cc_final: 0.9069 (p)
  outliers start: 43
  outliers final: 23
  residues processed: 229
  average time/residue: 0.5677
  time to fit residues: 142.6081
Evaluate side-chains
  219 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  473 VAL
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9980
   chunk 136 optimal weight:    6.9990
   chunk 146 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 121 optimal weight:    6.9990
   chunk 142 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    1.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 158 ASN
C 127 HIS
C 236 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.105800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.078015 restraints weight = 36773.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.55
r_work: 0.2753 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2614 r_free = 0.2614    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9108
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15309  Z= 0.149
  Angle     :  0.503  11.681  20873  Z= 0.263
  Chirality :  0.039   0.169   2315
  Planarity :  0.004   0.042   2515
  Dihedral  : 12.987 130.199   2627
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.50 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.27 (0.20), residues: 1711
  helix:  1.90 (0.18), residues: 833
  sheet:  0.33 (0.39), residues: 178
  loop : -0.27 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 287 
 TYR   0.018   0.001   TYR B 557 
 PHE   0.011   0.001   PHE A 105 
 TRP   0.018   0.001   TRP C  49 
 HIS   0.004   0.001   HIS B  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (15309)
  covalent geometry    : angle       0.50307 /  0.26 (20873)
  hydrogen bonds       : bond        0.04049 /  2.71 (  746)
  hydrogen bonds       : angle       4.18472 /  2.91 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 194
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6558 (pm20)
REVERT: A  168 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7177 (mtm110)
REVERT: A  181 GLU cc_start: 0.7901 (tp30) cc_final: 0.7193 (tp30)
REVERT: A  201 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8616 (mm)
REVERT: A  348 ILE cc_start: 0.8662 (tp) cc_final: 0.8450 (tp)
REVERT: A  543 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8983 (mt)
REVERT: B    1 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.6852 (tpt)
REVERT: B  375 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.8143 (m110)
REVERT: B  566 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (t)
REVERT: B  655 MET cc_start: 0.7183 (mmm) cc_final: 0.6972 (mmp)
REVERT: B  731 GLU cc_start: 0.8328 (tp30) cc_final: 0.8036 (mm-30)
REVERT: B  751 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: B  754 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (ptt180)
REVERT: C   53 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7226 (mpt)
REVERT: C  146 ASP cc_start: 0.8589 (p0) cc_final: 0.8236 (p0)
REVERT: G   11 SER cc_start: 0.4678 (OUTLIER) cc_final: 0.4387 (p)
REVERT: G   20 THR cc_start: 0.9373 (m) cc_final: 0.9086 (p)
  outliers start: 44
  outliers final: 25
  residues processed: 222
  average time/residue: 0.5370
  time to fit residues: 130.7151
Evaluate side-chains
  225 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 191
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  383 ASP
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  375 ASN
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  754 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue   87 ASP
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 15 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9990
   chunk 134 optimal weight:    8.9990
   chunk 25 optimal weight:    0.2980
   chunk 17 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 129 optimal weight:    0.2980
   chunk 26 optimal weight:    0.4980
   chunk 73 optimal weight:    5.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.108460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.080070 restraints weight = 37865.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.2925 rms_B_bonded: 2.67
r_work: 0.2785 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9027
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.077  15309  Z= 0.102
  Angle     :  0.486  12.141  20873  Z= 0.257
  Chirality :  0.038   0.162   2315
  Planarity :  0.004   0.040   2515
  Dihedral  : 12.926 128.786   2626
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 25.34 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.35 (0.20), residues: 1711
  helix:  1.97 (0.18), residues: 834
  sheet:  0.37 (0.39), residues: 178
  loop : -0.24 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 495 
 TYR   0.016   0.001   TYR B 557 
 PHE   0.016   0.001   PHE A  53 
 TRP   0.019   0.001   TRP C  49 
 HIS   0.003   0.000   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00224 /  0.10 (15309)
  covalent geometry    : angle       0.48583 /  0.26 (20873)
  hydrogen bonds       : bond        0.03602 /  2.40 (  746)
  hydrogen bonds       : angle       4.08984 /  2.84 ( 2065)

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

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

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3422 Ramachandran restraints generated.
    1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 197
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6489 (pm20)
REVERT: A  134 LYS cc_start: 0.8298 (mmmt) cc_final: 0.8095 (tptm)
REVERT: A  168 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.6929 (mtm110)
REVERT: A  181 GLU cc_start: 0.7881 (tp30) cc_final: 0.7177 (tp30)
REVERT: A  201 ILE cc_start: 0.8791 (mm) cc_final: 0.8585 (mm)
REVERT: A  348 ILE cc_start: 0.8682 (tp) cc_final: 0.8468 (tp)
REVERT: B    1 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6736 (tpt)
REVERT: B  566 THR cc_start: 0.8771 (OUTLIER) cc_final: 0.8526 (t)
REVERT: B  731 GLU cc_start: 0.8205 (tp30) cc_final: 0.7977 (mm-30)
REVERT: B  751 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: B  754 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7534 (ptt180)
REVERT: C   15 ARG cc_start: 0.7625 (mmm160) cc_final: 0.7392 (tpt170)
REVERT: C   53 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7066 (mpt)
REVERT: C  146 ASP cc_start: 0.8396 (p0) cc_final: 0.8049 (p0)
REVERT: G   11 SER cc_start: 0.4662 (OUTLIER) cc_final: 0.4401 (p)
REVERT: G   20 THR cc_start: 0.9315 (m) cc_final: 0.9062 (p)
  outliers start: 34
  outliers final: 22
  residues processed: 221
  average time/residue: 0.5443
  time to fit residues: 131.7423
Evaluate side-chains
  218 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 190
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   63 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  517 VAL
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  624 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  202 GLN
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  302 ILE
Chi-restraints excluded: chain B residue  307 THR
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  610 CYS
Chi-restraints excluded: chain B residue  615 LEU
Chi-restraints excluded: chain B residue  754 ARG
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain G residue    4 SER
Chi-restraints excluded: chain G residue   11 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 134 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 137 optimal weight:    5.9990
   chunk 37 optimal weight:    0.4980
   chunk 142 optimal weight:    6.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 556 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.108236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.081224 restraints weight = 25310.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.11
r_work: 0.2826 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2700 r_free = 0.2700    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9064
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.073  15309  Z= 0.109
  Angle     :  0.477   8.571  20873  Z= 0.255
  Chirality :  0.038   0.161   2315
  Planarity :  0.004   0.047   2515
  Dihedral  : 12.901 127.203   2626
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 25.41 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.23 %
    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:  1.33 (0.20), residues: 1711
  helix:  1.95 (0.18), residues: 834
  sheet:  0.35 (0.39), residues: 178
  loop : -0.24 (0.23), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 584 
 TYR   0.017   0.001   TYR B 557 
 PHE   0.014   0.001   PHE A 105 
 TRP   0.016   0.001   TRP C  49 
 HIS   0.002   0.001   HIS A 713 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 (15309)
  covalent geometry    : angle       0.47656 /  0.25 (20873)
  hydrogen bonds       : bond        0.03630 /  2.42 (  746)
  hydrogen bonds       : angle       4.09075 /  2.85 ( 2065)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4558.23 seconds
wall clock time: 78 minutes 28.28 seconds (4708.28 seconds total)