Starting phenix.real_space_refine
on Fri Jul  3 10:05:31 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ai5_11791/07_2026/7ai5_11791.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      50      5.49       5
     S      58      5.16       5
     C    8258      2.51       5
     N    2382      2.21       5
     O    2628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13376
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 788, 6206
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 35, 'TRANS': 752}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 788, 6206
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 35, 'TRANS': 752}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 457
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "D"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 445
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.70, per 1000 atoms: 0.20
  Number of scatterers: 13376
  At special positions: 0
  Unit cell: (127.53, 128.7, 115.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P      50     15.00
     O    2628      8.00
     N    2382      7.00
     C    8258      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 448.6 milliseconds
  

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2952

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 14 sheets defined
      51.3% alpha, 13.0% beta
      22 base pairs and 37 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 24
      removed outlier: 3.682A  pdb=" N   HIS A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 51
    Processing helix  chain 'A' and resid 75 through 86
      removed outlier: 3.824A  pdb=" N   TYR A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'A' and resid 162 through 174
    Processing helix  chain 'A' and resid 186 through 191
      removed outlier: 4.257A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 204
    Processing helix  chain 'A' and resid 205 through 218
      removed outlier: 3.646A  pdb=" N   ALA A 209 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 230 through 249
      removed outlier: 3.597A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 266
    Processing helix  chain 'A' and resid 270 through 277
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.843A  pdb=" N   VAL A 294 " --> pdb=" O   THR A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 313
    Processing helix  chain 'A' and resid 317 through 332
      removed outlier: 3.889A  pdb=" N   LEU A 321 " --> pdb=" O   ASP A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 344
      Proline residue:  A 340  - end of helix
      removed outlier: 3.927A  pdb=" N   GLN A 344 " --> pdb=" O   PRO A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
    Processing helix  chain 'A' and resid 361 through 385
      removed outlier: 3.657A  pdb=" N   ARG A 367 " --> pdb=" O   ARG A 363 " (cutoff:3.500A)
      Proline residue:  A 376  - end of helix
      removed outlier: 3.796A  pdb=" N   THR A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 398
      removed outlier: 3.506A  pdb=" N   GLN A 391 " --> pdb=" O   SER A 387 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 430 through 442
      removed outlier: 3.899A  pdb=" N   LEU A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ALA A 440 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 459
      removed outlier: 3.901A  pdb=" N   TYR A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 447 " --> pdb=" O   ALA A 443 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   GLU A 448 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 455 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 536
      removed outlier: 3.848A  pdb=" N   PHE A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 565
      removed outlier: 4.215A  pdb=" N   GLU A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LEU A 555 " --> pdb=" O   GLU A 551 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A 559 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 591
    Processing helix  chain 'A' and resid 621 through 635
      removed outlier: 3.848A  pdb=" N   THR A 627 " --> pdb=" O   TYR A 623 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR A 635 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 684
      removed outlier: 3.730A  pdb=" N   THR A 675 " --> pdb=" O   MET A 671 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU A 676 " --> pdb=" O   VAL A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 702 through 716
      removed outlier: 3.943A  pdb=" N   SER A 706 " --> pdb=" O   TYR A 702 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   ALA A 710 " --> pdb=" O   SER A 706 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU A 713 " --> pdb=" O   TRP A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
      removed outlier: 3.563A  pdb=" N   LYS A 738 " --> pdb=" O   GLN A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 776
      removed outlier: 4.078A  pdb=" N   ALA A 774 " --> pdb=" O   SER A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
    Processing helix  chain 'B' and resid 11 through 24
      removed outlier: 3.698A  pdb=" N   HIS B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 51
    Processing helix  chain 'B' and resid 72 through 74
      No H-bonds generated for 'chain 'B' and resid 72 through 74'
    Processing helix  chain 'B' and resid 75 through 86
      removed outlier: 3.816A  pdb=" N   TYR B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 162 through 174
    Processing helix  chain 'B' and resid 186 through 191
      removed outlier: 4.323A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 204
    Processing helix  chain 'B' and resid 205 through 218
      removed outlier: 3.638A  pdb=" N   ALA B 209 " --> pdb=" O   GLU B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 226
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.598A  pdb=" N   LEU B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA B 236 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 266
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.590A  pdb=" N   ASN B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 296
    Processing helix  chain 'B' and resid 300 through 313
    Processing helix  chain 'B' and resid 317 through 332
      removed outlier: 3.883A  pdb=" N   LEU B 321 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 344
      Proline residue:  B 340  - end of helix
      removed outlier: 3.948A  pdb=" N   GLN B 344 " --> pdb=" O   PRO B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 357
    Processing helix  chain 'B' and resid 361 through 385
      removed outlier: 3.664A  pdb=" N   ARG B 367 " --> pdb=" O   ARG B 363 " (cutoff:3.500A)
      Proline residue:  B 376  - end of helix
      removed outlier: 3.806A  pdb=" N   THR B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 398
      removed outlier: 3.532A  pdb=" N   GLN B 391 " --> pdb=" O   SER B 387 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   GLY B 398 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 430 through 442
      removed outlier: 3.955A  pdb=" N   LEU B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA B 440 " --> pdb=" O   TRP B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 459
      removed outlier: 3.887A  pdb=" N   TYR B 446 " --> pdb=" O   GLY B 442 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU B 447 " --> pdb=" O   ALA B 443 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU B 448 " --> pdb=" O   THR B 444 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG B 455 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 536
      removed outlier: 3.847A  pdb=" N   PHE B 532 " --> pdb=" O   TYR B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 566
      removed outlier: 4.299A  pdb=" N   GLU B 551 " --> pdb=" O   SER B 547 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LEU B 555 " --> pdb=" O   GLU B 551 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ALA B 559 " --> pdb=" O   LEU B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 591
    Processing helix  chain 'B' and resid 621 through 635
      removed outlier: 3.659A  pdb=" N   THR B 627 " --> pdb=" O   TYR B 623 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR B 635 " --> pdb=" O   ALA B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 671 through 684
      removed outlier: 3.725A  pdb=" N   THR B 675 " --> pdb=" O   MET B 671 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU B 676 " --> pdb=" O   VAL B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 700 through 716
      removed outlier: 3.850A  pdb=" N   ALA B 710 " --> pdb=" O   SER B 706 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 713 " --> pdb=" O   TRP B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 733
      No H-bonds generated for 'chain 'B' and resid 731 through 733'
    Processing helix  chain 'B' and resid 734 through 739
      removed outlier: 3.577A  pdb=" N   LYS B 738 " --> pdb=" O   GLN B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 776
      removed outlier: 4.045A  pdb=" N   ALA B 774 " --> pdb=" O   SER B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 800
      removed outlier: 3.613A  pdb=" N   SER B 800 " --> pdb=" O   LEU B 796 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58
      removed outlier: 4.310A  pdb=" N   ILE A  66 " --> pdb=" O   ARG A  58 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ILE A  71 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A  31 " --> pdb=" O   GLU A  38 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   PHE A  40 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  40 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   LEU A  28 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   CYS A  93 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   PHE A  30 " --> pdb=" O   CYS A  93 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   GLN A  95 " --> pdb=" O   PHE A  30 " (cutoff:3.500A)
      removed outlier: 8.762A  pdb=" N   ARG A  32 " --> pdb=" O   GLN A  95 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   VAL A 110 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.630A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA A 134 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 9.173A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   ILE A 136 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 135 " --> pdb=" O   ALA A 146 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   PHE A 155 " --> pdb=" O   THR A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269
      removed outlier: 6.952A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   THR A 655 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ARG A 652 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   LEU A 691 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 468
      removed outlier: 3.641A  pdb=" N   GLY A 466 " --> pdb=" O   TYR A 474 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   ALA A 498 " --> pdb=" O   THR A 494 " (cutoff:3.500A)
      removed outlier: 5.727A  pdb=" N   THR A 494 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ARG A 500 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 571 through 572
      removed outlier: 6.886A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LYS A 644 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   GLU A 582 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 4.903A  pdb=" N   ASN A 599 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 613
      removed outlier: 6.790A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   THR A 613 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   ALA A 749 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   ASN A 744 " --> pdb=" O   GLN A 763 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   GLN A 763 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   HIS A 746 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   SER A 761 " --> pdb=" O   HIS A 746 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   ASP A 748 " --> pdb=" O   MET A 759 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   MET A 759 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   HIS A 752 " --> pdb=" O   THR A 755 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   THR A 755 " --> pdb=" O   HIS A 752 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.273A  pdb=" N   GLU B  94 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   VAL B 110 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40
      removed outlier: 3.909A  pdb=" N   ILE B  66 " --> pdb=" O   ARG B  58 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 199
      removed outlier: 6.619A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   TYR B 180 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ALA B 134 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
      removed outlier: 9.212A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 134 " (cutoff:3.500A)
      removed outlier: 8.324A  pdb=" N   ILE B 136 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B 135 " --> pdb=" O   ALA B 146 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   TRP B 137 " --> pdb=" O   GLY B 144 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   PHE B 155 " --> pdb=" O   THR B 259 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 468
      removed outlier: 3.649A  pdb=" N   GLY B 466 " --> pdb=" O   TYR B 474 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ALA B 498 " --> pdb=" O   THR B 494 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   THR B 494 " --> pdb=" O   ALA B 498 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ARG B 500 " --> pdb=" O   ARG B 492 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 571 through 572
      removed outlier: 6.816A  pdb=" N   THR B 571 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LYS B 644 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   GLU B 582 " --> pdb=" O   ASN B 599 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ASN B 599 " --> pdb=" O   GLU B 582 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 609 through 613
      removed outlier: 6.792A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 652 through 657
      removed outlier: 6.313A  pdb=" N   ARG B 652 " --> pdb=" O   LEU B 689 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   LEU B 691 " --> pdb=" O   ARG B 652 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   PHE B 654 " --> pdb=" O   LEU B 691 " (cutoff:3.500A)
      removed outlier: 7.875A  pdb=" N   ASP B 693 " --> pdb=" O   PHE B 654 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   ARG B 656 " --> pdb=" O   ASP B 693 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 750 through 752
      removed outlier: 3.546A  pdb=" N   HIS B 752 " --> pdb=" O   THR B 755 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR B 755 " --> pdb=" O   HIS B 752 " (cutoff:3.500A)

    573 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      56 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      37 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2168
        1.30 -     1.44: 3618
        1.44 -     1.58: 7714
        1.58 -     1.72: 96
        1.72 -     1.86: 104
  Bond restraints: 13700
  Sorted by residual:
  bond pdb=" C   ILE A 650 "
       pdb=" O   ILE A 650 "
    ideal  model  delta    sigma   weight residual
    1.236  1.317 -0.080 1.04e-02 9.25e+03 5.99e+01
  bond pdb=" C   ILE A 636 "
       pdb=" O   ILE A 636 "
    ideal  model  delta    sigma   weight residual
    1.242  1.309 -0.067 1.13e-02 7.83e+03 3.55e+01
  bond pdb=" C   THR A 685 "
       pdb=" O   THR A 685 "
    ideal  model  delta    sigma   weight residual
    1.238  1.177  0.061 1.06e-02 8.90e+03 3.26e+01
  bond pdb=" C   PRO A 175 "
       pdb=" O   PRO A 175 "
    ideal  model  delta    sigma   weight residual
    1.235  1.165  0.070 1.30e-02 5.92e+03 2.87e+01
  bond pdb=" C   GLY A 780 "
       pdb=" O   GLY A 780 "
    ideal  model  delta    sigma   weight residual
    1.232  1.283 -0.051 1.03e-02 9.43e+03 2.49e+01
  ... (remaining 13695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 14615
        2.29 -     4.57: 3830
        4.57 -     6.86: 268
        6.86 -     9.14: 24
        9.14 -    11.43: 9
  Bond angle restraints: 18746
  Sorted by residual:
  angle pdb=" PB  ATP B 901 "
        pdb=" O3B ATP B 901 "
        pdb=" PG  ATP B 901 "
      ideal   model   delta    sigma   weight residual
     139.87  131.11    8.76 1.00e+00 1.00e+00 7.67e+01
  angle pdb=" C   PRO A 615 "
        pdb=" CA  PRO A 615 "
        pdb=" CB  PRO A 615 "
      ideal   model   delta    sigma   weight residual
     110.98   99.55   11.43 1.31e+00 5.83e-01 7.61e+01
  angle pdb=" PB  ATP A 901 "
        pdb=" O3B ATP A 901 "
        pdb=" PG  ATP A 901 "
      ideal   model   delta    sigma   weight residual
     139.87  131.37    8.50 1.00e+00 1.00e+00 7.23e+01
  angle pdb=" CA  PHE A 155 "
        pdb=" CB  PHE A 155 "
        pdb=" CG  PHE A 155 "
      ideal   model   delta    sigma   weight residual
     113.80  121.58   -7.78 1.00e+00 1.00e+00 6.05e+01
  angle pdb=" N   SER A 621 "
        pdb=" CA  SER A 621 "
        pdb=" C   SER A 621 "
      ideal   model   delta    sigma   weight residual
     111.14  119.34   -8.20 1.08e+00 8.57e-01 5.76e+01
  ... (remaining 18741 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 7126
       17.99 -    35.97: 701
       35.97 -    53.96: 318
       53.96 -    71.95: 71
       71.95 -    89.93: 20
  Dihedral angle restraints: 8236
    sinusoidal: 3660
      harmonic: 4576
  Sorted by residual:
  dihedral pdb=" C   THR A 273 "
           pdb=" N   THR A 273 "
           pdb=" CA  THR A 273 "
           pdb=" CB  THR A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -109.90  -12.10     0      2.50e+00 1.60e-01 2.34e+01
  dihedral pdb=" C   PRO A 615 "
           pdb=" N   PRO A 615 "
           pdb=" CA  PRO A 615 "
           pdb=" CB  PRO A 615 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -108.69  -12.01     0      2.50e+00 1.60e-01 2.31e+01
  dihedral pdb=" C   ASN B 593 "
           pdb=" N   ASN B 593 "
           pdb=" CA  ASN B 593 "
           pdb=" CB  ASN B 593 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.92  -10.68     0      2.50e+00 1.60e-01 1.82e+01
  ... (remaining 8233 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1217
       0.088 -    0.177: 741
       0.177 -    0.265: 140
       0.265 -    0.353: 21
       0.353 -    0.442: 3
  Chirality restraints: 2122
  Sorted by residual:
  chirality pdb=" CB  VAL A 640 "
            pdb=" CA  VAL A 640 "
            pdb=" CG1 VAL A 640 "
            pdb=" CG2 VAL A 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.19   -0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" CA  ALA A 766 "
            pdb=" N   ALA A 766 "
            pdb=" C   ALA A 766 "
            pdb=" CB  ALA A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.87   -0.38 2.00e-01 2.50e+01 3.69e+00
  chirality pdb=" CA  VAL B 657 "
            pdb=" N   VAL B 657 "
            pdb=" C   VAL B 657 "
            pdb=" CB  VAL B 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.81   -0.37 2.00e-01 2.50e+01 3.36e+00
  ... (remaining 2119 not shown)

  Planarity restraints: 2288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 635 "    0.021 2.00e-02 2.50e+03   3.60e-02 2.59e+01
        pdb=" CG  TYR A 635 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 635 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 635 "   -0.072 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 635 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 635 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 635 "    0.041 2.00e-02 2.50e+03
        pdb=" OH  TYR A 635 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 132 "    0.022 2.00e-02 2.50e+03   4.59e-02 2.10e+01
        pdb=" C   LEU A 132 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   LEU A 132 "    0.029 2.00e-02 2.50e+03
        pdb=" N   LEU A 133 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 309 "   -0.020 2.00e-02 2.50e+03   4.20e-02 1.76e+01
        pdb=" C   ARG A 309 "    0.073 2.00e-02 2.50e+03
        pdb=" O   ARG A 309 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   TRP A 310 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 2285 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 5547
        2.96 -     3.44: 13307
        3.44 -     3.93: 22952
        3.93 -     4.41: 26036
        4.41 -     4.90: 40766
  Nonbonded interactions: 108608
  Sorted by model distance:
  nonbonded pdb=" N   ASN B 616 "
            pdb=" O   ASN B 616 "
     model   vdw
     2.472 2.496
  nonbonded pdb=" OD1 ASP B 296 "
            pdb=" OG1 THR B 298 "
     model   vdw
     2.479 3.040
  nonbonded pdb=" O   ASP B  98 "
            pdb=" OG1 THR B 101 "
     model   vdw
     2.484 3.040
  nonbonded pdb=" N   GLU A 731 "
            pdb=" OE1 GLU A 731 "
     model   vdw
     2.511 3.120
  nonbonded pdb=" N   TYR A 702 "
            pdb=" N   ASP A 703 "
     model   vdw
     2.521 2.560
  ... (remaining 108603 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.060
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
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      :  0.014   0.080  13700  Z= 1.035
  Angle     :  1.844  11.431  18746  Z= 1.376
  Chirality :  0.105   0.442   2122
  Planarity :  0.008   0.054   2288
  Dihedral  : 17.870  89.933   5284
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.60 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.34 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.18), residues: 1568
  helix: -0.83 (0.18), residues: 665
  sheet: -1.88 (0.36), residues: 137
  loop : -1.65 (0.19), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.002   ARG A 652 
 TYR   0.072   0.007   TYR A 635 
 PHE   0.070   0.006   PHE A  36 
 TRP   0.022   0.005   TRP A 310 
 HIS   0.040   0.006   HIS A 728 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01388 /  1.03 (13700)
  covalent geometry    : angle       1.84365 /  1.38 (18746)
  hydrogen bonds       : bond        0.22752 / 15.18 (  629)
  hydrogen bonds       : angle       8.08747 /  5.52 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 289
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.8196 (mmm) cc_final: 0.7995 (mmm)
REVERT: A  187 MET cc_start: 0.8972 (mmm) cc_final: 0.8043 (mmt)
REVERT: A  269 MET cc_start: 0.7066 (mtm) cc_final: 0.6796 (mmm)
REVERT: A  365 LEU cc_start: 0.9283 (mt) cc_final: 0.8913 (mm)
REVERT: A  574 ASP cc_start: 0.8482 (m-30) cc_final: 0.7958 (p0)
REVERT: A  674 MET cc_start: 0.8911 (mmm) cc_final: 0.8248 (mmt)
REVERT: A  686 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8191 (tp30)
REVERT: A  730 PHE cc_start: 0.8006 (t80) cc_final: 0.7601 (t80)
REVERT: B   88 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8122 (mm-30)
REVERT: B  171 GLN cc_start: 0.9430 (tt0) cc_final: 0.9138 (tt0)
REVERT: B  173 THR cc_start: 0.8876 (p) cc_final: 0.8183 (p)
REVERT: B  258 ILE cc_start: 0.9151 (tt) cc_final: 0.8771 (tt)
REVERT: B  441 ASP cc_start: 0.7806 (m-30) cc_final: 0.7556 (p0)
REVERT: B  603 LEU cc_start: 0.8852 (mt) cc_final: 0.8559 (mm)
REVERT: B  616 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (m-40)
REVERT: B  633 MET cc_start: 0.8694 (mtm) cc_final: 0.8272 (mtm)
REVERT: B  703 ASP cc_start: 0.8564 (t70) cc_final: 0.7949 (t70)
REVERT: B  730 PHE cc_start: 0.7230 (t80) cc_final: 0.6937 (t80)
REVERT: B  732 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8244 (mt)
  outliers start: 15
  outliers final: 3
  residues processed: 300
  average time/residue: 0.1268
  time to fit residues: 52.2199
Evaluate side-chains
  160 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 155
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 248 GLN
A 276 ASN
** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 557 ASN
A 599 ASN
B 616 ASN
B 683 ASN
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.078544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.058121 restraints weight = 84188.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.059937 restraints weight = 49772.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.061135 restraints weight = 33735.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.061918 restraints weight = 25495.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.062352 restraints weight = 21002.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13700  Z= 0.196
  Angle     :  0.747  10.764  18746  Z= 0.399
  Chirality :  0.047   0.294   2122
  Planarity :  0.006   0.071   2288
  Dihedral  : 17.705  88.152   2230
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.90 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.19), residues: 1568
  helix:  0.16 (0.18), residues: 721
  sheet: -1.57 (0.31), residues: 184
  loop : -1.43 (0.22), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 579 
 TYR   0.022   0.002   TYR B  31 
 PHE   0.025   0.002   PHE A 372 
 TRP   0.021   0.003   TRP A 137 
 HIS   0.011   0.001   HIS B 370 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.20 (13700)
  covalent geometry    : angle       0.74665 /  0.40 (18746)
  hydrogen bonds       : bond        0.06134 /  4.10 (  629)
  hydrogen bonds       : angle       5.61142 /  3.82 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.8899 (mmm) cc_final: 0.8620 (mmt)
REVERT: A  508 GLU cc_start: 0.9306 (tt0) cc_final: 0.9024 (pt0)
REVERT: A  574 ASP cc_start: 0.8450 (m-30) cc_final: 0.7689 (p0)
REVERT: A  575 LYS cc_start: 0.8195 (mttt) cc_final: 0.7913 (mmmt)
REVERT: A  739 MET cc_start: 0.7704 (mtp) cc_final: 0.7230 (ttt)
REVERT: A  744 ASN cc_start: 0.8582 (t0) cc_final: 0.8254 (t0)
REVERT: A  771 TYR cc_start: 0.8060 (p90) cc_final: 0.7603 (p90)
REVERT: B  128 ARG cc_start: 0.6325 (mtt180) cc_final: 0.5831 (ptp-110)
REVERT: B  243 TYR cc_start: 0.8636 (t80) cc_final: 0.8378 (t80)
REVERT: B  441 ASP cc_start: 0.8743 (m-30) cc_final: 0.8325 (p0)
REVERT: B  514 LEU cc_start: 0.8548 (pp) cc_final: 0.8284 (pp)
REVERT: B  629 LEU cc_start: 0.7581 (mt) cc_final: 0.7375 (mt)
REVERT: B  633 MET cc_start: 0.8819 (mtm) cc_final: 0.8285 (mtm)
REVERT: B  759 MET cc_start: 0.7476 (mmt) cc_final: 0.6761 (mmp)
REVERT: B  771 TYR cc_start: 0.7577 (p90) cc_final: 0.7205 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 0.1282
  time to fit residues: 33.0637
Evaluate side-chains
  115 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0980
   chunk 126 optimal weight:   20.0000
   chunk 7 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 154 optimal weight:    4.9990
   chunk 134 optimal weight:    0.1980
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 282 ASN
** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 763 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.089930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.066160 restraints weight = 68284.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.067823 restraints weight = 43866.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.068970 restraints weight = 32216.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.069728 restraints weight = 25706.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.070257 restraints weight = 21907.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  13700  Z= 0.144
  Angle     :  0.682  20.714  18746  Z= 0.354
  Chirality :  0.044   0.190   2122
  Planarity :  0.005   0.060   2288
  Dihedral  : 17.767  88.444   2230
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.05 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.20), residues: 1568
  helix:  0.55 (0.19), residues: 712
  sheet: -1.37 (0.32), residues: 197
  loop : -1.26 (0.22), residues: 659

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 579 
 TYR   0.023   0.002   TYR B  31 
 PHE   0.019   0.002   PHE A  30 
 TRP   0.024   0.002   TRP B 436 
 HIS   0.005   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (13700)
  covalent geometry    : angle       0.68169 /  0.35 (18746)
  hydrogen bonds       : bond        0.04830 /  3.26 (  629)
  hydrogen bonds       : angle       5.13386 /  3.55 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 HIS cc_start: 0.7852 (p-80) cc_final: 0.7528 (p90)
REVERT: A  187 MET cc_start: 0.9104 (mmm) cc_final: 0.8820 (mmt)
REVERT: A  239 CYS cc_start: 0.8722 (t) cc_final: 0.8354 (m)
REVERT: A  508 GLU cc_start: 0.9459 (tt0) cc_final: 0.9200 (pt0)
REVERT: A  574 ASP cc_start: 0.8573 (m-30) cc_final: 0.7704 (p0)
REVERT: A  575 LYS cc_start: 0.8223 (mttt) cc_final: 0.7950 (mmmt)
REVERT: A  771 TYR cc_start: 0.8180 (p90) cc_final: 0.7634 (p90)
REVERT: B   68 MET cc_start: 0.2918 (tmm) cc_final: 0.2489 (tmm)
REVERT: B   88 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8769 (mm-30)
REVERT: B  243 TYR cc_start: 0.8110 (t80) cc_final: 0.7903 (t80)
REVERT: B  432 GLU cc_start: 0.9208 (pm20) cc_final: 0.8852 (pm20)
REVERT: B  441 ASP cc_start: 0.8641 (m-30) cc_final: 0.8276 (p0)
REVERT: B  609 MET cc_start: 0.7942 (tpp) cc_final: 0.7643 (tpp)
REVERT: B  629 LEU cc_start: 0.7706 (mt) cc_final: 0.7367 (mt)
REVERT: B  633 MET cc_start: 0.8758 (mtm) cc_final: 0.8211 (mtm)
REVERT: B  771 TYR cc_start: 0.7513 (p90) cc_final: 0.7134 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 162
  average time/residue: 0.1185
  time to fit residues: 28.3706
Evaluate side-chains
  116 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 146 optimal weight:   10.0000
   chunk 125 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 156 optimal weight:   50.0000
   chunk 26 optimal weight:    8.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    4.7188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 242 GLN
** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
A 683 ASN
** A 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  78 ASN
** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 GLN
B 526 GLN
B 616 ASN
B 746 HIS
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.073143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.052773 restraints weight = 87388.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.054251 restraints weight = 53691.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.055241 restraints weight = 37987.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.055852 restraints weight = 29734.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.056386 restraints weight = 25117.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079  13700  Z= 0.307
  Angle     :  0.828  10.472  18746  Z= 0.425
  Chirality :  0.047   0.272   2122
  Planarity :  0.006   0.057   2288
  Dihedral  : 17.908  89.364   2230
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.66 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.19), residues: 1568
  helix:  0.02 (0.18), residues: 734
  sheet: -1.52 (0.30), residues: 200
  loop : -1.52 (0.22), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 350 
 TYR   0.025   0.002   TYR B 729 
 PHE   0.018   0.003   PHE A 572 
 TRP   0.008   0.002   TRP B 310 
 HIS   0.009   0.002   HIS B 746 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00659 /  0.31 (13700)
  covalent geometry    : angle       0.82769 /  0.42 (18746)
  hydrogen bonds       : bond        0.05332 /  3.65 (  629)
  hydrogen bonds       : angle       5.49883 /  3.81 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 CYS cc_start: 0.8686 (t) cc_final: 0.8329 (m)
REVERT: A  372 PHE cc_start: 0.8539 (m-10) cc_final: 0.8327 (m-80)
REVERT: A  445 ASP cc_start: 0.9167 (t0) cc_final: 0.8765 (p0)
REVERT: A  574 ASP cc_start: 0.8457 (m-30) cc_final: 0.7685 (p0)
REVERT: A  575 LYS cc_start: 0.8177 (mttt) cc_final: 0.7845 (mmmt)
REVERT: A  617 MET cc_start: 0.8889 (mmp) cc_final: 0.8589 (mmm)
REVERT: A  671 MET cc_start: 0.8659 (tpt) cc_final: 0.8334 (tpp)
REVERT: A  771 TYR cc_start: 0.8521 (p90) cc_final: 0.7941 (p90)
REVERT: B   68 MET cc_start: 0.4343 (tmm) cc_final: 0.4011 (tmm)
REVERT: B  243 TYR cc_start: 0.8366 (t80) cc_final: 0.7854 (t80)
REVERT: B  609 MET cc_start: 0.7947 (tpp) cc_final: 0.7448 (tpp)
REVERT: B  633 MET cc_start: 0.8929 (mtm) cc_final: 0.8487 (mtm)
REVERT: B  717 ASN cc_start: 0.8969 (m-40) cc_final: 0.8736 (m-40)
REVERT: B  759 MET cc_start: 0.7475 (mmt) cc_final: 0.7025 (mmp)
REVERT: B  771 TYR cc_start: 0.8167 (p90) cc_final: 0.7499 (p90)
  outliers start: 2
  outliers final: 1
  residues processed: 141
  average time/residue: 0.1237
  time to fit residues: 25.7090
Evaluate side-chains
  100 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    8.9990
   chunk 72 optimal weight:    0.3980
   chunk 107 optimal weight:    0.7980
   chunk 152 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 136 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
A 763 GLN
B 281 GLN
B 526 GLN
B 763 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.076321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.055777 restraints weight = 85304.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.057358 restraints weight = 52178.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.058429 restraints weight = 36651.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.059147 restraints weight = 28445.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.059623 restraints weight = 23832.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13700  Z= 0.128
  Angle     :  0.625   8.151  18746  Z= 0.328
  Chirality :  0.043   0.199   2122
  Planarity :  0.005   0.058   2288
  Dihedral  : 17.828  89.737   2230
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.52 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.20), residues: 1568
  helix:  0.73 (0.19), residues: 723
  sheet: -1.17 (0.32), residues: 188
  loop : -1.30 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 584 
 TYR   0.022   0.001   TYR A 528 
 PHE   0.019   0.002   PHE B 155 
 TRP   0.005   0.001   TRP A 137 
 HIS   0.005   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 (13700)
  covalent geometry    : angle       0.62487 /  0.33 (18746)
  hydrogen bonds       : bond        0.04000 /  2.64 (  629)
  hydrogen bonds       : angle       4.91379 /  3.42 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 CYS cc_start: 0.8631 (t) cc_final: 0.8198 (m)
REVERT: A  372 PHE cc_start: 0.8633 (m-10) cc_final: 0.8323 (m-80)
REVERT: A  445 ASP cc_start: 0.9219 (t0) cc_final: 0.8821 (p0)
REVERT: A  527 LEU cc_start: 0.9592 (mt) cc_final: 0.9388 (pp)
REVERT: A  617 MET cc_start: 0.8724 (mmp) cc_final: 0.8448 (mmm)
REVERT: A  671 MET cc_start: 0.8558 (tpt) cc_final: 0.8211 (tpp)
REVERT: A  771 TYR cc_start: 0.8364 (p90) cc_final: 0.7706 (p90)
REVERT: B   13 MET cc_start: 0.6821 (ppp) cc_final: 0.6443 (ppp)
REVERT: B  243 TYR cc_start: 0.8320 (t80) cc_final: 0.8113 (t80)
REVERT: B  281 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8166 (tm-30)
REVERT: B  441 ASP cc_start: 0.8879 (m-30) cc_final: 0.8624 (m-30)
REVERT: B  609 MET cc_start: 0.7895 (tpp) cc_final: 0.7500 (tpp)
REVERT: B  633 MET cc_start: 0.8892 (mtm) cc_final: 0.8235 (mtm)
REVERT: B  759 MET cc_start: 0.7819 (mmt) cc_final: 0.7447 (mmp)
REVERT: B  771 TYR cc_start: 0.7689 (p90) cc_final: 0.7066 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1284
  time to fit residues: 27.1277
Evaluate side-chains
  109 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 130 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 128 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN
B 763 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.074640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.054199 restraints weight = 85547.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.055719 restraints weight = 52950.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.056749 restraints weight = 37489.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.057431 restraints weight = 29283.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.057910 restraints weight = 24656.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  13700  Z= 0.181
  Angle     :  0.635   7.200  18746  Z= 0.334
  Chirality :  0.043   0.286   2122
  Planarity :  0.005   0.049   2288
  Dihedral  : 17.764  89.979   2230
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.60 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.20), residues: 1568
  helix:  0.75 (0.19), residues: 728
  sheet: -1.24 (0.31), residues: 200
  loop : -1.32 (0.22), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  58 
 TYR   0.020   0.001   TYR A 528 
 PHE   0.015   0.002   PHE B 184 
 TRP   0.004   0.001   TRP A 310 
 HIS   0.006   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.18 (13700)
  covalent geometry    : angle       0.63479 /  0.33 (18746)
  hydrogen bonds       : bond        0.04096 /  2.75 (  629)
  hydrogen bonds       : angle       5.01471 /  3.50 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 CYS cc_start: 0.8775 (t) cc_final: 0.8308 (m)
REVERT: A  368 MET cc_start: 0.8890 (ptp) cc_final: 0.8631 (ptt)
REVERT: A  372 PHE cc_start: 0.8727 (m-10) cc_final: 0.8426 (m-80)
REVERT: A  445 ASP cc_start: 0.9273 (t0) cc_final: 0.8894 (p0)
REVERT: A  617 MET cc_start: 0.8785 (mmp) cc_final: 0.8526 (mmm)
REVERT: A  671 MET cc_start: 0.8629 (tpt) cc_final: 0.8253 (tpp)
REVERT: A  759 MET cc_start: 0.8210 (mpp) cc_final: 0.7906 (mpp)
REVERT: A  771 TYR cc_start: 0.8220 (p90) cc_final: 0.7653 (p90)
REVERT: B   13 MET cc_start: 0.6904 (ppp) cc_final: 0.6526 (ppp)
REVERT: B   68 MET cc_start: 0.4507 (tmm) cc_final: 0.4010 (tmm)
REVERT: B  441 ASP cc_start: 0.8878 (m-30) cc_final: 0.8619 (m-30)
REVERT: B  633 MET cc_start: 0.8932 (mtm) cc_final: 0.8315 (mtm)
REVERT: B  759 MET cc_start: 0.7926 (mmp) cc_final: 0.7600 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1219
  time to fit residues: 24.4811
Evaluate side-chains
  105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 148 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 71 optimal weight:    0.3980
   chunk 133 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 154 optimal weight:    8.9990
   chunk 151 optimal weight:    0.2980
   chunk 0 optimal weight:   20.0000
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.086127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.062927 restraints weight = 70947.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.064304 restraints weight = 47665.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.065299 restraints weight = 36172.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.065990 restraints weight = 29700.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.066447 restraints weight = 25706.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13700  Z= 0.118
  Angle     :  0.610   7.399  18746  Z= 0.319
  Chirality :  0.043   0.217   2122
  Planarity :  0.005   0.068   2288
  Dihedral  : 17.681  89.854   2230
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.20), residues: 1568
  helix:  1.01 (0.19), residues: 728
  sheet: -1.09 (0.32), residues: 193
  loop : -1.24 (0.22), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 697 
 TYR   0.021   0.001   TYR A 528 
 PHE   0.020   0.001   PHE B 155 
 TRP   0.007   0.001   TRP A 310 
 HIS   0.005   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 (13700)
  covalent geometry    : angle       0.61005 /  0.32 (18746)
  hydrogen bonds       : bond        0.03670 /  2.44 (  629)
  hydrogen bonds       : angle       4.78683 /  3.34 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 PHE cc_start: 0.8705 (m-10) cc_final: 0.8426 (m-80)
REVERT: A  445 ASP cc_start: 0.9293 (t0) cc_final: 0.8881 (p0)
REVERT: A  574 ASP cc_start: 0.8557 (m-30) cc_final: 0.8010 (p0)
REVERT: A  617 MET cc_start: 0.8580 (mmp) cc_final: 0.8378 (mmm)
REVERT: A  671 MET cc_start: 0.8492 (tpt) cc_final: 0.8124 (tpp)
REVERT: A  674 MET cc_start: 0.8939 (mmp) cc_final: 0.8276 (mmt)
REVERT: A  771 TYR cc_start: 0.8153 (p90) cc_final: 0.7578 (p90)
REVERT: B   13 MET cc_start: 0.6945 (ppp) cc_final: 0.6587 (ppp)
REVERT: B  397 MET cc_start: 0.8882 (mtm) cc_final: 0.8462 (mmm)
REVERT: B  441 ASP cc_start: 0.8799 (m-30) cc_final: 0.8546 (m-30)
REVERT: B  609 MET cc_start: 0.7790 (tpp) cc_final: 0.7506 (tpp)
REVERT: B  633 MET cc_start: 0.8734 (mtm) cc_final: 0.8139 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1172
  time to fit residues: 23.5316
Evaluate side-chains
  107 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 146 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 28 optimal weight:    6.9990
   chunk 129 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 150 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.074445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.054095 restraints weight = 85543.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.055603 restraints weight = 52585.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.056617 restraints weight = 37232.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.057298 restraints weight = 29093.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.057785 restraints weight = 24509.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13700  Z= 0.174
  Angle     :  0.630   6.851  18746  Z= 0.329
  Chirality :  0.043   0.215   2122
  Planarity :  0.005   0.075   2288
  Dihedral  : 17.694  89.739   2230
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.20), residues: 1568
  helix:  0.99 (0.19), residues: 727
  sheet: -1.15 (0.32), residues: 205
  loop : -1.28 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 697 
 TYR   0.018   0.002   TYR B  31 
 PHE   0.041   0.002   PHE B  36 
 TRP   0.006   0.001   TRP A 310 
 HIS   0.005   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.17 (13700)
  covalent geometry    : angle       0.62976 /  0.33 (18746)
  hydrogen bonds       : bond        0.03927 /  2.67 (  629)
  hydrogen bonds       : angle       4.85643 /  3.39 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 PHE cc_start: 0.8780 (m-10) cc_final: 0.8543 (m-80)
REVERT: A  445 ASP cc_start: 0.9300 (t0) cc_final: 0.8903 (p0)
REVERT: A  574 ASP cc_start: 0.8665 (m-30) cc_final: 0.8041 (p0)
REVERT: A  617 MET cc_start: 0.8787 (mmp) cc_final: 0.8250 (tpt)
REVERT: A  671 MET cc_start: 0.8556 (tpt) cc_final: 0.8183 (tpp)
REVERT: A  674 MET cc_start: 0.8956 (mmp) cc_final: 0.8355 (mmt)
REVERT: A  759 MET cc_start: 0.8511 (mpp) cc_final: 0.8154 (mpp)
REVERT: A  771 TYR cc_start: 0.8138 (p90) cc_final: 0.7620 (p90)
REVERT: B  397 MET cc_start: 0.9022 (mtm) cc_final: 0.8628 (mmm)
REVERT: B  441 ASP cc_start: 0.8910 (m-30) cc_final: 0.8650 (m-30)
REVERT: B  609 MET cc_start: 0.7827 (tpp) cc_final: 0.7406 (tpp)
REVERT: B  633 MET cc_start: 0.8953 (mtm) cc_final: 0.8361 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1169
  time to fit residues: 23.4276
Evaluate side-chains
  105 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0970
   chunk 108 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 99 optimal weight:    4.9990
   chunk 120 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.9584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN
B 763 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.074625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.054250 restraints weight = 85809.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.055767 restraints weight = 52948.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.056798 restraints weight = 37389.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.057479 restraints weight = 29165.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.057980 restraints weight = 24533.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.5158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13700  Z= 0.143
  Angle     :  0.603   7.586  18746  Z= 0.316
  Chirality :  0.042   0.203   2122
  Planarity :  0.005   0.060   2288
  Dihedral  : 17.679  89.254   2230
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.76 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.20), residues: 1568
  helix:  1.11 (0.19), residues: 727
  sheet: -1.08 (0.32), residues: 205
  loop : -1.23 (0.23), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 697 
 TYR   0.023   0.001   TYR B  31 
 PHE   0.029   0.002   PHE B  36 
 TRP   0.006   0.001   TRP A 310 
 HIS   0.006   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.14 (13700)
  covalent geometry    : angle       0.60318 /  0.32 (18746)
  hydrogen bonds       : bond        0.03641 /  2.45 (  629)
  hydrogen bonds       : angle       4.73168 /  3.30 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  372 PHE cc_start: 0.8664 (m-10) cc_final: 0.8456 (m-80)
REVERT: A  445 ASP cc_start: 0.9222 (t0) cc_final: 0.8828 (p0)
REVERT: A  574 ASP cc_start: 0.8524 (m-30) cc_final: 0.7970 (p0)
REVERT: A  671 MET cc_start: 0.8485 (tpt) cc_final: 0.8126 (tpp)
REVERT: A  674 MET cc_start: 0.8941 (mmp) cc_final: 0.8353 (mmt)
REVERT: A  759 MET cc_start: 0.8516 (mpp) cc_final: 0.8275 (mpp)
REVERT: A  771 TYR cc_start: 0.8260 (p90) cc_final: 0.7730 (p90)
REVERT: B   13 MET cc_start: 0.6728 (ppp) cc_final: 0.6467 (ppp)
REVERT: B  397 MET cc_start: 0.8870 (mtm) cc_final: 0.8563 (mmm)
REVERT: B  441 ASP cc_start: 0.8904 (m-30) cc_final: 0.8644 (m-30)
REVERT: B  633 MET cc_start: 0.8886 (mtm) cc_final: 0.8315 (mtm)
REVERT: B  759 MET cc_start: 0.8027 (mmm) cc_final: 0.7810 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1125
  time to fit residues: 22.5139
Evaluate side-chains
  106 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    7.9990
   chunk 132 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 137 optimal weight:    2.9990
   chunk 116 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN
** B 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.072904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.052865 restraints weight = 86604.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.054235 restraints weight = 55225.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.055188 restraints weight = 39953.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.055838 restraints weight = 31602.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.056277 restraints weight = 26737.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  13700  Z= 0.207
  Angle     :  0.667   7.055  18746  Z= 0.347
  Chirality :  0.043   0.207   2122
  Planarity :  0.005   0.054   2288
  Dihedral  : 17.719  89.373   2230
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.20), residues: 1568
  helix:  0.88 (0.19), residues: 728
  sheet: -1.04 (0.32), residues: 197
  loop : -1.38 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 367 
 TYR   0.019   0.002   TYR B  31 
 PHE   0.030   0.002   PHE B  36 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.006   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.21 (13700)
  covalent geometry    : angle       0.66739 /  0.35 (18746)
  hydrogen bonds       : bond        0.04134 /  2.84 (  629)
  hydrogen bonds       : angle       4.91747 /  3.42 ( 1714)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 CYS cc_start: 0.8701 (t) cc_final: 0.8328 (m)
REVERT: A  445 ASP cc_start: 0.9333 (t0) cc_final: 0.8908 (p0)
REVERT: A  574 ASP cc_start: 0.8605 (m-30) cc_final: 0.7939 (p0)
REVERT: A  617 MET cc_start: 0.8696 (mmp) cc_final: 0.8271 (tpt)
REVERT: A  671 MET cc_start: 0.8638 (tpt) cc_final: 0.8234 (tpp)
REVERT: A  674 MET cc_start: 0.8964 (mmp) cc_final: 0.8358 (mmt)
REVERT: A  759 MET cc_start: 0.8589 (mpp) cc_final: 0.8147 (mpp)
REVERT: B  397 MET cc_start: 0.8881 (mtm) cc_final: 0.8631 (mmm)
REVERT: B  441 ASP cc_start: 0.8845 (m-30) cc_final: 0.8560 (m-30)
REVERT: B  617 MET cc_start: 0.7816 (mmt) cc_final: 0.7507 (ttm)
REVERT: B  633 MET cc_start: 0.8951 (mtm) cc_final: 0.8354 (mtm)
REVERT: B  739 MET cc_start: 0.8899 (tmm) cc_final: 0.8670 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0938
  time to fit residues: 18.1218
Evaluate side-chains
  100 residues out of total 1312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 58 optimal weight:    0.3980
   chunk 7 optimal weight:    5.9990
   chunk 154 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 134 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 526 GLN
B 763 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.074971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.054553 restraints weight = 85804.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.056100 restraints weight = 53167.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.057131 restraints weight = 37389.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.057853 restraints weight = 29098.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.058339 restraints weight = 24384.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.5449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13700  Z= 0.117
  Angle     :  0.608   8.226  18746  Z= 0.317
  Chirality :  0.042   0.207   2122
  Planarity :  0.005   0.051   2288
  Dihedral  : 17.660  89.274   2230
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.38 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.20), residues: 1568
  helix:  1.08 (0.19), residues: 724
  sheet: -1.00 (0.32), residues: 198
  loop : -1.23 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 788 
 TYR   0.023   0.001   TYR B  31 
 PHE   0.028   0.002   PHE A 372 
 TRP   0.006   0.001   TRP B 709 
 HIS   0.006   0.001   HIS B  24 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 (13700)
  covalent geometry    : angle       0.60795 /  0.32 (18746)
  hydrogen bonds       : bond        0.03527 /  2.35 (  629)
  hydrogen bonds       : angle       4.69583 /  3.26 ( 1714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2304.15 seconds
wall clock time: 40 minutes 41.45 seconds (2441.45 seconds total)