Starting phenix.real_space_refine
on Wed Feb  4 19:49:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9opy_70730/02_2026/9opy_70730.cif"
  }
  resolution = 3.51
  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=   0.006 sd=   0.092
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      97      5.16       5
     C    8020      2.51       5
     N    2053      2.21       5
     O    2218      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12388
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 6172
          Classifications: {'peptide': 774}
          Incomplete info: {'backbone_only': 2}
          Link IDs: {'PTRANS': 40, 'TRANS': 733}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 6216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 796, 6216
          Classifications: {'peptide': 796}
          Link IDs: {'PTRANS': 42, 'TRANS': 753}
          Chain breaks: 2
  Time building chain proxies: 2.57, per 1000 atoms: 0.21
  Number of scatterers: 12388
  At special positions: 0
  Unit cell: (92.158, 99.946, 184.316, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      97     16.00
     O    2218      8.00
     N    2053      7.00
     C    8020      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: 0.83
  Conformation dependent library (CDL) restraints added in 580.5 milliseconds
  

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2980

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 17 sheets defined
      54.2% alpha, 11.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 62
      removed outlier: 3.990A  pdb=" N   TYR A  62 " --> pdb=" O   CYS A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 85
      removed outlier: 3.872A  pdb=" N   TYR A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 143 through 156
      removed outlier: 3.606A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LEU A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.643A  pdb=" N   LEU A 171 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
      removed outlier: 3.601A  pdb=" N   HIS A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 228
      removed outlier: 3.668A  pdb=" N   ALA A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 250 through 267
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 4.234A  pdb=" N   PHE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.382A  pdb=" N   ARG A 317 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 382 through 403
      removed outlier: 4.208A  pdb=" N   TYR A 386 " --> pdb=" O   GLU A 382 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   SER A 387 " --> pdb=" O   ARG A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 563 through 590
    Processing helix  chain 'A' and resid 593 through 600
    Processing helix  chain 'A' and resid 601 through 615
    Processing helix  chain 'A' and resid 617 through 622
    Processing helix  chain 'A' and resid 626 through 635
    Processing helix  chain 'A' and resid 635 through 656
      removed outlier: 3.728A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   CYS A 644 " --> pdb=" O   CYS A 640 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 645 " --> pdb=" O   PHE A 641 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL A 656 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 665
    Processing helix  chain 'A' and resid 665 through 675
    Processing helix  chain 'A' and resid 676 through 701
      removed outlier: 3.560A  pdb=" N   GLY A 696 " --> pdb=" O   ILE A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 749
      removed outlier: 3.954A  pdb=" N   LEU A 734 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A 735 " --> pdb=" O   ASN A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 757 through 781
      removed outlier: 4.120A  pdb=" N   PHE A 761 " --> pdb=" O   ASN A 757 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A 781 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 818
      removed outlier: 4.507A  pdb=" N   ILE A 790 " --> pdb=" O   VAL A 786 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE A 808 " --> pdb=" O   SER A 804 " (cutoff:3.500A)
      Proline residue:  A 810  - end of helix
    Processing helix  chain 'A' and resid 819 through 822
    Processing helix  chain 'A' and resid 823 through 829
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 47 through 51
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 3.791A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 118
      removed outlier: 4.085A  pdb=" N   MET B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE B 116 " --> pdb=" O   SER B 112 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 134
    Processing helix  chain 'B' and resid 146 through 159
      removed outlier: 4.079A  pdb=" N   PHE B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
    Processing helix  chain 'B' and resid 189 through 204
      removed outlier: 3.664A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 233
    Processing helix  chain 'B' and resid 249 through 266
    Processing helix  chain 'B' and resid 276 through 291
      removed outlier: 3.553A  pdb=" N   TYR B 286 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY B 291 " --> pdb=" O   SER B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 312
    Processing helix  chain 'B' and resid 333 through 345
    Processing helix  chain 'B' and resid 346 through 353
      removed outlier: 6.162A  pdb=" N   ALA B 349 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B 350 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 375
      removed outlier: 3.514A  pdb=" N   CYS B 372 " --> pdb=" O   CYS B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 380
    Processing helix  chain 'B' and resid 381 through 386
      removed outlier: 3.775A  pdb=" N   LEU B 385 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 415
    Processing helix  chain 'B' and resid 429 through 438
      removed outlier: 4.146A  pdb=" N   GLU B 435 " --> pdb=" O   TRP B 431 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ASN B 436 " --> pdb=" O   GLN B 432 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   TYR B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 492
    Processing helix  chain 'B' and resid 573 through 598
      removed outlier: 3.559A  pdb=" N   CYS B 582 " --> pdb=" O   LEU B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 608
      removed outlier: 4.054A  pdb=" N   GLN B 605 " --> pdb=" O   SER B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 625
      removed outlier: 3.570A  pdb=" N   LEU B 624 " --> pdb=" O   GLY B 620 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   SER B 625 " --> pdb=" O   LEU B 621 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 629
    Processing helix  chain 'B' and resid 634 through 666
      removed outlier: 3.559A  pdb=" N   LEU B 639 " --> pdb=" O   SER B 635 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   GLN B 642 " --> pdb=" O   CYS B 638 " (cutoff:3.500A)
      Proline residue:  B 643  - end of helix
      Proline residue:  B 648  - end of helix
      removed outlier: 3.865A  pdb=" N   THR B 655 " --> pdb=" O   GLY B 651 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU B 656 " --> pdb=" O   CYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 682
      removed outlier: 5.200A  pdb=" N   TRP B 676 " --> pdb=" O   SER B 672 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B 682 " --> pdb=" O   CYS B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 708
    Processing helix  chain 'B' and resid 731 through 738
      removed outlier: 3.637A  pdb=" N   GLY B 736 " --> pdb=" O   VAL B 733 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B 737 " --> pdb=" O   SER B 734 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL B 738 " --> pdb=" O   LEU B 735 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 754
    Processing helix  chain 'B' and resid 764 through 788
      removed outlier: 4.275A  pdb=" N   GLY B 768 " --> pdb=" O   ASN B 764 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   VAL B 784 " --> pdb=" O   TRP B 780 " (cutoff:3.500A)
      Proline residue:  B 785  - end of helix
    Processing helix  chain 'B' and resid 791 through 793
      No H-bonds generated for 'chain 'B' and resid 791 through 793'
    Processing helix  chain 'B' and resid 794 through 815
      removed outlier: 3.733A  pdb=" N   VAL B 798 " --> pdb=" O   TYR B 794 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 799 " --> pdb=" O   GLN B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 815 through 825
    Processing helix  chain 'B' and resid 826 through 829
    Processing helix  chain 'B' and resid 830 through 835
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.288A  pdb=" N   TYR A  33 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   GLU A  97 " --> pdb=" O   TYR A  33 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   LEU A  35 " --> pdb=" O   GLU A  97 " (cutoff:3.500A)
      removed outlier: 7.735A  pdb=" N   VAL A  99 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA A 137 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   GLN A 161 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 239
      removed outlier: 7.512A  pdb=" N   ILE A 206 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   GLN A 237 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   VAL A 208 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A 271 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 5.602A  pdb=" N   PHE A 322 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ILE A 450 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 431
    Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 507
    Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 527
      removed outlier: 6.148A  pdb=" N   ASN A 527 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   GLU A 534 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 543
    Processing sheet with id=AA8, first strand: chain 'A' and resid 555 through 557
      removed outlier: 6.049A  pdb=" N   GLN A 555 " --> pdb=" O   THR A 716 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   VAL A 718 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 31
      removed outlier: 6.332A  pdb=" N   TYR B  35 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   ASP B  98 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   LEU B  37 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   PHE B 100 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLY B  39 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B 140 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   GLN B 164 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.492A  pdb=" N   VAL B 209 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLU B 240 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ALA B 211 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   LEU B 242 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   GLY B 213 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL B 270 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER B 214 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 8.539A  pdb=" N   PHE B 324 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   VAL B 321 " --> pdb=" O   TRP B 466 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   MET B 465 " --> pdb=" O   THR B 477 " (cutoff:3.500A)
      removed outlier: 5.460A  pdb=" N   THR B 477 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   VAL B 467 " --> pdb=" O   LEU B 475 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   LEU B 475 " --> pdb=" O   VAL B 467 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 442 through 444
      removed outlier: 3.556A  pdb=" N   LEU B 447 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 512 through 513
    Processing sheet with id=AB5, first strand: chain 'B' and resid 516 through 517
      removed outlier: 3.653A  pdb=" N   CYS B 523 " --> pdb=" O   LYS B 517 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 533 through 534
    Processing sheet with id=AB7, first strand: chain 'B' and resid 550 through 551
    Processing sheet with id=AB8, first strand: chain 'B' and resid 563 through 565

    632 hydrogen bonds defined for protein.
    1770 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3919
        1.34 -     1.46: 2736
        1.46 -     1.58: 5925
        1.58 -     1.70: 0
        1.70 -     1.81: 136
  Bond restraints: 12716
  Sorted by residual:
  bond pdb=" N   TYR A 724 "
       pdb=" CA  TYR A 724 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.034 1.29e-02 6.01e+03 6.92e+00
  bond pdb=" N   ASN A 726 "
       pdb=" CA  ASN A 726 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.16e-02 7.43e+03 6.79e+00
  bond pdb=" N   ASN A 731 "
       pdb=" CA  ASN A 731 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.20e-02 6.94e+03 6.40e+00
  bond pdb=" N   PHE A 730 "
       pdb=" CA  PHE A 730 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.34e+00
  bond pdb=" N   ARG A 725 "
       pdb=" CA  ARG A 725 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.23e-02 6.61e+03 5.89e+00
  ... (remaining 12711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 16267
        1.15 -     2.30: 860
        2.30 -     3.44: 169
        3.44 -     4.59: 33
        4.59 -     5.74: 11
  Bond angle restraints: 17340
  Sorted by residual:
  angle pdb=" N   LYS A 750 "
        pdb=" CA  LYS A 750 "
        pdb=" C   LYS A 750 "
      ideal   model   delta    sigma   weight residual
     111.07  115.81   -4.74 1.07e+00 8.73e-01 1.96e+01
  angle pdb=" N   ASN A 723 "
        pdb=" CA  ASN A 723 "
        pdb=" C   ASN A 723 "
      ideal   model   delta    sigma   weight residual
     110.70  105.53    5.17 1.55e+00 4.16e-01 1.11e+01
  angle pdb=" CA  ASN A 723 "
        pdb=" C   ASN A 723 "
        pdb=" O   ASN A 723 "
      ideal   model   delta    sigma   weight residual
     122.44  118.22    4.22 1.34e+00 5.57e-01 9.91e+00
  angle pdb=" C   ARG A 230 "
        pdb=" N   ASP A 231 "
        pdb=" CA  ASP A 231 "
      ideal   model   delta    sigma   weight residual
     126.86  121.97    4.89 1.57e+00 4.06e-01 9.68e+00
  angle pdb=" CA  THR A 732 "
        pdb=" CB  THR A 732 "
        pdb=" OG1 THR A 732 "
      ideal   model   delta    sigma   weight residual
     109.60  105.04    4.56 1.50e+00 4.44e-01 9.23e+00
  ... (remaining 17335 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 6977
       16.79 -    33.58: 407
       33.58 -    50.38: 74
       50.38 -    67.17: 16
       67.17 -    83.96: 9
  Dihedral angle restraints: 7483
    sinusoidal: 2883
      harmonic: 4600
  Sorted by residual:
  dihedral pdb=" CA  ILE B 142 "
           pdb=" C   ILE B 142 "
           pdb=" N   GLY B 143 "
           pdb=" CA  GLY B 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.12  -24.88     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" CA  ARG A 413 "
           pdb=" C   ARG A 413 "
           pdb=" N   VAL A 414 "
           pdb=" CA  VAL A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.77   24.23     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  LEU A 313 "
           pdb=" C   LEU A 313 "
           pdb=" N   THR A 314 "
           pdb=" CA  THR A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.64  -23.36     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 7480 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1241
       0.029 -    0.058: 476
       0.058 -    0.087: 158
       0.087 -    0.116: 88
       0.116 -    0.144: 19
  Chirality restraints: 1982
  Sorted by residual:
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  LEU A 728 "
            pdb=" N   LEU A 728 "
            pdb=" C   LEU A 728 "
            pdb=" CB  LEU A 728 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.55e-01
  ... (remaining 1979 not shown)

  Planarity restraints: 2190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 725 "   -0.265 9.50e-02 1.11e+02   1.19e-01 8.63e+00
        pdb=" NE  ARG A 725 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 725 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 725 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 725 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 802 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.89e+00
        pdb=" C   ALA A 802 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ALA A 802 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 803 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 805 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   LEU A 805 "    0.027 2.00e-02 2.50e+03
        pdb=" O   LEU A 805 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLY A 806 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2187 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3630
        2.82 -     3.34: 12021
        3.34 -     3.86: 19954
        3.86 -     4.38: 23388
        4.38 -     4.90: 39654
  Nonbonded interactions: 98647
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 327 "
            pdb=" OD1 ASP B 462 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   VAL B 419 "
            pdb=" OG  SER B 420 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OD1 ASN B 675 "
            pdb=" N   TRP B 676 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" O   ASN A 477 "
            pdb=" ND2 ASN A 477 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" N   ALA B 299 "
            pdb=" O   LEU B 322 "
     model   vdw
     2.404 3.120
  ... (remaining 98642 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.450
  Find NCS groups from input model:        0.090
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
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      :  0.003   0.034  12716  Z= 0.167
  Angle     :  0.623   5.741  17340  Z= 0.359
  Chirality :  0.039   0.144   1982
  Planarity :  0.005   0.119   2190
  Dihedral  : 11.821  83.962   4503
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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:  0.01 (0.20), residues: 1555
  helix:  0.53 (0.18), residues: 737
  sheet: -0.64 (0.35), residues: 184
  loop : -0.24 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.017   0.001   TYR A 675 
 PHE   0.015   0.001   PHE A 743 
 TRP   0.013   0.001   TRP A 205 
 HIS   0.004   0.001   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12716)
  covalent geometry    : angle       0.62268 (17340)
  hydrogen bonds       : bond        0.15601 (  632)
  hydrogen bonds       : angle       6.17329 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLU cc_start: 0.7234 (tt0) cc_final: 0.6788 (tt0)
REVERT: A  239 THR cc_start: 0.9187 (m) cc_final: 0.8842 (p)
REVERT: A  307 ASP cc_start: 0.7530 (t0) cc_final: 0.7312 (t0)
REVERT: A  556 LEU cc_start: 0.9061 (mm) cc_final: 0.8731 (mm)
REVERT: A  609 THR cc_start: 0.9272 (m) cc_final: 0.9043 (p)
REVERT: A  745 PHE cc_start: 0.8582 (m-10) cc_final: 0.8173 (m-10)
REVERT: A  748 MET cc_start: 0.8866 (mmm) cc_final: 0.8611 (mmm)
REVERT: A  774 VAL cc_start: 0.9118 (t) cc_final: 0.8813 (m)
REVERT: B   70 LEU cc_start: 0.7824 (tp) cc_final: 0.7555 (tt)
REVERT: B   76 MET cc_start: 0.8525 (ttt) cc_final: 0.8316 (ttt)
REVERT: B  437 MET cc_start: 0.8963 (ttm) cc_final: 0.8636 (ttm)
REVERT: B  687 TRP cc_start: 0.7545 (m100) cc_final: 0.7309 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1044
  time to fit residues: 40.3232
Evaluate side-chains
  157 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.0060
   overall best weight:    0.4874

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

Flipped N/Q/H residues before XYZ refinement:
A 397 HIS
A 400 HIS
A 447 HIS
B  27 GLN
B  58 ASN
B 231 ASN
B 537 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.160237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.112292 restraints weight = 20548.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113703 restraints weight = 14595.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113414 restraints weight = 11654.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.113553 restraints weight = 11140.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113718 restraints weight = 10548.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12716  Z= 0.130
  Angle     :  0.631  12.652  17340  Z= 0.323
  Chirality :  0.043   0.191   1982
  Planarity :  0.004   0.041   2190
  Dihedral  :  5.269  24.020   1681
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  7.89 %
    Favored  : 90.73 %
  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:  0.52 (0.21), residues: 1555
  helix:  1.06 (0.19), residues: 754
  sheet: -0.61 (0.36), residues: 189
  loop : -0.09 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 445 
 TYR   0.021   0.001   TYR A 675 
 PHE   0.037   0.002   PHE A 605 
 TRP   0.013   0.001   TRP B 303 
 HIS   0.004   0.001   HIS B 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (12716)
  covalent geometry    : angle       0.63074 (17340)
  hydrogen bonds       : bond        0.04842 (  632)
  hydrogen bonds       : angle       4.90294 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLU cc_start: 0.7378 (tt0) cc_final: 0.6965 (tt0)
REVERT: A  239 THR cc_start: 0.9190 (m) cc_final: 0.8815 (p)
REVERT: A  307 ASP cc_start: 0.7602 (t0) cc_final: 0.7353 (t0)
REVERT: A  460 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6535 (t0)
REVERT: A  577 PHE cc_start: 0.7869 (t80) cc_final: 0.7631 (t80)
REVERT: A  697 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6475 (tmm)
REVERT: A  774 VAL cc_start: 0.9092 (t) cc_final: 0.8867 (m)
REVERT: A  817 PHE cc_start: 0.7888 (t80) cc_final: 0.7589 (t80)
REVERT: B   70 LEU cc_start: 0.7826 (tp) cc_final: 0.7570 (tt)
REVERT: B   76 MET cc_start: 0.8426 (ttt) cc_final: 0.8221 (ttt)
REVERT: B  110 MET cc_start: 0.8452 (mmm) cc_final: 0.8220 (mmm)
REVERT: B  647 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7898 (mm)
REVERT: B  664 PHE cc_start: 0.8854 (t80) cc_final: 0.8619 (t80)
REVERT: B  755 LEU cc_start: 0.8901 (pp) cc_final: 0.8684 (mm)
REVERT: B  771 PHE cc_start: 0.8089 (m-80) cc_final: 0.7885 (m-80)
  outliers start: 19
  outliers final: 11
  residues processed: 196
  average time/residue: 0.0870
  time to fit residues: 26.9006
Evaluate side-chains
  169 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 ASN
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  647 LEU
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 142 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 151 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
B 231 ASN
B 396 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.156320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.105423 restraints weight = 21094.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.107585 restraints weight = 15917.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.108005 restraints weight = 12005.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108093 restraints weight = 11465.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.108239 restraints weight = 11504.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12716  Z= 0.196
  Angle     :  0.655  10.330  17340  Z= 0.333
  Chirality :  0.045   0.263   1982
  Planarity :  0.004   0.044   2190
  Dihedral  :  5.127  23.980   1681
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.85 %
    Favored  : 87.69 %
  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:  0.58 (0.21), residues: 1555
  helix:  1.21 (0.19), residues: 750
  sheet: -0.80 (0.35), residues: 201
  loop : -0.10 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 473 
 TYR   0.023   0.002   TYR A 675 
 PHE   0.042   0.002   PHE A 730 
 TRP   0.013   0.001   TRP B 303 
 HIS   0.006   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (12716)
  covalent geometry    : angle       0.65507 (17340)
  hydrogen bonds       : bond        0.04735 (  632)
  hydrogen bonds       : angle       4.76532 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.5807 (tpp) cc_final: 0.5581 (tpp)
REVERT: A   81 GLU cc_start: 0.7459 (tt0) cc_final: 0.7026 (tt0)
REVERT: A  239 THR cc_start: 0.9361 (m) cc_final: 0.8915 (p)
REVERT: A  433 ASP cc_start: 0.7446 (t0) cc_final: 0.7244 (t70)
REVERT: A  460 ASN cc_start: 0.7192 (OUTLIER) cc_final: 0.6563 (t0)
REVERT: A  556 LEU cc_start: 0.8787 (mm) cc_final: 0.8393 (mm)
REVERT: A  558 PHE cc_start: 0.8139 (p90) cc_final: 0.7577 (p90)
REVERT: A  690 MET cc_start: 0.8900 (tmm) cc_final: 0.8540 (ptt)
REVERT: A  697 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6178 (tmm)
REVERT: A  748 MET cc_start: 0.8652 (mmm) cc_final: 0.8113 (mmt)
REVERT: B   70 LEU cc_start: 0.7979 (tp) cc_final: 0.7701 (tt)
REVERT: B  110 MET cc_start: 0.8599 (mmm) cc_final: 0.8376 (mmm)
REVERT: B  619 LEU cc_start: 0.7743 (tp) cc_final: 0.7483 (tp)
REVERT: B  647 LEU cc_start: 0.8037 (mm) cc_final: 0.7832 (mm)
REVERT: B  664 PHE cc_start: 0.8849 (t80) cc_final: 0.8637 (t80)
REVERT: B  755 LEU cc_start: 0.8791 (pp) cc_final: 0.8585 (mm)
REVERT: B  771 PHE cc_start: 0.8085 (m-80) cc_final: 0.7883 (m-80)
  outliers start: 34
  outliers final: 19
  residues processed: 194
  average time/residue: 0.0892
  time to fit residues: 26.7017
Evaluate side-chains
  182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 ASN
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  573 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 153 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 147 optimal weight:    4.9990
   chunk 141 optimal weight:    8.9990
   chunk 132 optimal weight:   10.0000
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0170
   chunk 28 optimal weight:    3.9990
   chunk 155 optimal weight:    1.9990
   overall best weight:    1.5222

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 189 HIS
A 528 HIS
A 634 GLN
B 231 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.155990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107436 restraints weight = 21061.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.109061 restraints weight = 16274.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.108813 restraints weight = 11764.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.108868 restraints weight = 12397.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.109257 restraints weight = 11396.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12716  Z= 0.169
  Angle     :  0.652  12.791  17340  Z= 0.324
  Chirality :  0.044   0.210   1982
  Planarity :  0.004   0.046   2190
  Dihedral  :  4.942  23.325   1681
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.73 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.22), residues: 1555
  helix:  1.39 (0.19), residues: 740
  sheet: -0.77 (0.35), residues: 203
  loop : -0.06 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 473 
 TYR   0.018   0.002   TYR A 724 
 PHE   0.022   0.002   PHE A 684 
 TRP   0.015   0.001   TRP B 303 
 HIS   0.005   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12716)
  covalent geometry    : angle       0.65237 (17340)
  hydrogen bonds       : bond        0.04352 (  632)
  hydrogen bonds       : angle       4.63371 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 171
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 THR cc_start: 0.9379 (m) cc_final: 0.8972 (p)
REVERT: A  460 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6537 (t0)
REVERT: A  556 LEU cc_start: 0.8791 (mm) cc_final: 0.8396 (mm)
REVERT: A  697 MET cc_start: 0.6521 (OUTLIER) cc_final: 0.6008 (tmm)
REVERT: A  745 PHE cc_start: 0.8440 (m-10) cc_final: 0.7748 (m-10)
REVERT: A  748 MET cc_start: 0.8505 (mmm) cc_final: 0.7982 (mmt)
REVERT: A  805 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8616 (mp)
REVERT: B   70 LEU cc_start: 0.8004 (tp) cc_final: 0.7687 (tt)
REVERT: B  110 MET cc_start: 0.8563 (mmm) cc_final: 0.8351 (mmm)
REVERT: B  619 LEU cc_start: 0.7724 (tp) cc_final: 0.7473 (tp)
REVERT: B  647 LEU cc_start: 0.8019 (mm) cc_final: 0.7793 (mm)
REVERT: B  771 PHE cc_start: 0.7949 (m-80) cc_final: 0.7711 (m-80)
  outliers start: 33
  outliers final: 23
  residues processed: 191
  average time/residue: 0.0858
  time to fit residues: 25.5040
Evaluate side-chains
  185 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 159
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 ASN
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  573 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  663 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 115 optimal weight:   10.0000
   chunk 83 optimal weight:    0.0770
   chunk 106 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 129 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
A 528 HIS
B 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.157281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.108369 restraints weight = 21189.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.109810 restraints weight = 15620.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109551 restraints weight = 12290.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.109806 restraints weight = 11530.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.110012 restraints weight = 11098.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12716  Z= 0.122
  Angle     :  0.638  14.932  17340  Z= 0.310
  Chirality :  0.043   0.355   1982
  Planarity :  0.004   0.056   2190
  Dihedral  :  4.697  22.116   1681
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.24 %
    Favored  : 85.08 %
  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:  0.73 (0.22), residues: 1555
  helix:  1.47 (0.19), residues: 754
  sheet: -0.76 (0.35), residues: 203
  loop : -0.23 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 674 
 TYR   0.017   0.001   TYR A 389 
 PHE   0.025   0.001   PHE B 750 
 TRP   0.015   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12716)
  covalent geometry    : angle       0.63840 (17340)
  hydrogen bonds       : bond        0.03910 (  632)
  hydrogen bonds       : angle       4.50185 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8962 (m-40) cc_final: 0.8320 (m-40)
REVERT: A  239 THR cc_start: 0.9370 (m) cc_final: 0.8950 (p)
REVERT: A  460 ASN cc_start: 0.7215 (OUTLIER) cc_final: 0.6410 (t0)
REVERT: A  556 LEU cc_start: 0.8829 (mm) cc_final: 0.8412 (mm)
REVERT: A  661 MET cc_start: 0.6542 (tpp) cc_final: 0.6227 (tmm)
REVERT: A  697 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6107 (tmm)
REVERT: A  724 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7445 (t80)
REVERT: A  745 PHE cc_start: 0.8461 (m-10) cc_final: 0.8110 (m-10)
REVERT: A  748 MET cc_start: 0.8602 (mmm) cc_final: 0.7838 (mmt)
REVERT: B   70 LEU cc_start: 0.7911 (tp) cc_final: 0.7564 (tt)
REVERT: B  110 MET cc_start: 0.8304 (mmm) cc_final: 0.8052 (mmm)
REVERT: B  541 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.6218 (m-80)
REVERT: B  619 LEU cc_start: 0.7746 (tp) cc_final: 0.7464 (tp)
REVERT: B  647 LEU cc_start: 0.8027 (mm) cc_final: 0.7816 (mm)
REVERT: B  771 PHE cc_start: 0.8050 (m-80) cc_final: 0.7803 (m-80)
  outliers start: 37
  outliers final: 18
  residues processed: 193
  average time/residue: 0.0969
  time to fit residues: 28.7201
Evaluate side-chains
  180 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 ASN
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  520 HIS
Chi-restraints excluded: chain B residue  541 PHE
Chi-restraints excluded: chain B residue  573 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  625 SER
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 141 optimal weight:    9.9990
   chunk 58 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 147 optimal weight:    7.9990
   chunk 72 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 149 optimal weight:    4.9990
   chunk 128 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
A 757 ASN
B 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.153516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.111741 restraints weight = 21112.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111520 restraints weight = 20676.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.108155 restraints weight = 15284.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108379 restraints weight = 14640.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.108916 restraints weight = 13034.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12716  Z= 0.239
  Angle     :  0.716  15.429  17340  Z= 0.352
  Chirality :  0.046   0.335   1982
  Planarity :  0.004   0.055   2190
  Dihedral  :  4.949  25.579   1681
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 13.18 %
    Favored  : 83.71 %
  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 (0.22), residues: 1555
  helix:  1.37 (0.19), residues: 746
  sheet: -0.97 (0.35), residues: 207
  loop : -0.29 (0.27), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 473 
 TYR   0.021   0.002   TYR A 389 
 PHE   0.024   0.002   PHE A 684 
 TRP   0.012   0.001   TRP B 303 
 HIS   0.007   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 (12716)
  covalent geometry    : angle       0.71649 (17340)
  hydrogen bonds       : bond        0.04588 (  632)
  hydrogen bonds       : angle       4.70727 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 159
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.6517 (t0)
REVERT: A  556 LEU cc_start: 0.8648 (mm) cc_final: 0.8254 (mm)
REVERT: A  697 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5582 (tmm)
REVERT: A  724 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6891 (t80)
REVERT: A  745 PHE cc_start: 0.8388 (m-10) cc_final: 0.7985 (m-10)
REVERT: A  748 MET cc_start: 0.8284 (mmm) cc_final: 0.7655 (mmt)
REVERT: B   70 LEU cc_start: 0.7989 (tp) cc_final: 0.7572 (tt)
REVERT: B  110 MET cc_start: 0.8606 (mmm) cc_final: 0.8380 (mmm)
REVERT: B  619 LEU cc_start: 0.7678 (tp) cc_final: 0.7402 (tp)
  outliers start: 43
  outliers final: 33
  residues processed: 185
  average time/residue: 0.0948
  time to fit residues: 27.3347
Evaluate side-chains
  188 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 152
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  460 ASN
Chi-restraints excluded: chain A residue  501 SER
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  771 THR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue   78 MET
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  520 HIS
Chi-restraints excluded: chain B residue  542 THR
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  573 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  663 THR
Chi-restraints excluded: chain B residue  733 VAL
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  803 ILE
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 138 optimal weight:    3.9990
   chunk 45 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 123 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
A 511 HIS
A 528 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.156570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.110104 restraints weight = 21003.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.109860 restraints weight = 15708.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.109631 restraints weight = 13229.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.109733 restraints weight = 12982.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.109932 restraints weight = 12672.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12716  Z= 0.123
  Angle     :  0.667  15.057  17340  Z= 0.318
  Chirality :  0.043   0.383   1982
  Planarity :  0.004   0.056   2190
  Dihedral  :  4.666  22.516   1681
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.77 %
    Favored  : 82.91 %
  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:  0.73 (0.22), residues: 1555
  helix:  1.54 (0.19), residues: 755
  sheet: -0.88 (0.35), residues: 204
  loop : -0.29 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 767 
 TYR   0.019   0.001   TYR A 669 
 PHE   0.033   0.001   PHE A 684 
 TRP   0.018   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (12716)
  covalent geometry    : angle       0.66728 (17340)
  hydrogen bonds       : bond        0.03868 (  632)
  hydrogen bonds       : angle       4.57022 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 159
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 THR cc_start: 0.9472 (m) cc_final: 0.9046 (p)
REVERT: A  556 LEU cc_start: 0.8734 (mm) cc_final: 0.8302 (mm)
REVERT: A  682 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7690 (ptt)
REVERT: A  697 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5881 (tmm)
REVERT: A  724 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7457 (t80)
REVERT: A  745 PHE cc_start: 0.8472 (m-10) cc_final: 0.8020 (m-10)
REVERT: A  748 MET cc_start: 0.8586 (mmm) cc_final: 0.7886 (mmt)
REVERT: B   70 LEU cc_start: 0.7904 (tp) cc_final: 0.7564 (tt)
REVERT: B  110 MET cc_start: 0.8477 (mmm) cc_final: 0.8216 (mmm)
REVERT: B  585 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7492 (mm)
REVERT: B  619 LEU cc_start: 0.7691 (tp) cc_final: 0.7379 (tp)
REVERT: B  714 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7914 (m)
REVERT: B  771 PHE cc_start: 0.8046 (m-80) cc_final: 0.7566 (m-80)
  outliers start: 32
  outliers final: 18
  residues processed: 177
  average time/residue: 0.0947
  time to fit residues: 26.1623
Evaluate side-chains
  179 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  573 VAL
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 137 optimal weight:    0.0060
   chunk 3 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0370
   chunk 154 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 4 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
B 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.157916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.110815 restraints weight = 21131.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112703 restraints weight = 14820.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.112528 restraints weight = 12017.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112810 restraints weight = 12797.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112771 restraints weight = 12117.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12716  Z= 0.108
  Angle     :  0.688  19.139  17340  Z= 0.318
  Chirality :  0.044   0.439   1982
  Planarity :  0.004   0.056   2190
  Dihedral  :  4.414  20.934   1681
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.55 %
    Favored  : 83.13 %
  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:  0.86 (0.22), residues: 1555
  helix:  1.65 (0.19), residues: 753
  sheet: -0.81 (0.36), residues: 204
  loop : -0.21 (0.27), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 506 
 TYR   0.017   0.001   TYR A 669 
 PHE   0.024   0.001   PHE B 614 
 TRP   0.018   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (12716)
  covalent geometry    : angle       0.68762 (17340)
  hydrogen bonds       : bond        0.03774 (  632)
  hydrogen bonds       : angle       4.46795 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 163
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ASN cc_start: 0.8881 (m-40) cc_final: 0.8449 (m-40)
REVERT: A  239 THR cc_start: 0.9352 (m) cc_final: 0.8924 (p)
REVERT: A  556 LEU cc_start: 0.8705 (mm) cc_final: 0.8308 (mm)
REVERT: A  669 TYR cc_start: 0.7890 (t80) cc_final: 0.7227 (t80)
REVERT: A  682 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7457 (ptt)
REVERT: A  697 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5759 (tmm)
REVERT: A  724 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7331 (t80)
REVERT: A  745 PHE cc_start: 0.8609 (m-10) cc_final: 0.8175 (m-10)
REVERT: A  748 MET cc_start: 0.8574 (mmm) cc_final: 0.7849 (mmt)
REVERT: B   70 LEU cc_start: 0.7813 (tp) cc_final: 0.7497 (tt)
REVERT: B  110 MET cc_start: 0.8391 (mmm) cc_final: 0.8149 (mmm)
REVERT: B  344 LEU cc_start: 0.8622 (tp) cc_final: 0.8262 (pp)
REVERT: B  585 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7506 (mm)
REVERT: B  619 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7321 (tp)
REVERT: B  714 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7811 (m)
  outliers start: 32
  outliers final: 20
  residues processed: 181
  average time/residue: 0.0916
  time to fit residues: 25.9848
Evaluate side-chains
  179 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  520 HIS
Chi-restraints excluded: chain B residue  567 LEU
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 141 optimal weight:   10.0000
   chunk 149 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 397 HIS
A 528 HIS
B 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.155427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.106943 restraints weight = 21101.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.107221 restraints weight = 16092.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.107666 restraints weight = 12454.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.107792 restraints weight = 11877.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.108001 restraints weight = 11369.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12716  Z= 0.172
  Angle     :  0.724  16.807  17340  Z= 0.339
  Chirality :  0.046   0.405   1982
  Planarity :  0.004   0.060   2190
  Dihedral  :  4.532  21.694   1681
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.35 %
    Favored  : 82.33 %
  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:  0.68 (0.22), residues: 1555
  helix:  1.52 (0.19), residues: 752
  sheet: -0.96 (0.36), residues: 197
  loop : -0.31 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 632 
 TYR   0.015   0.001   TYR A 389 
 PHE   0.033   0.002   PHE B 750 
 TRP   0.011   0.001   TRP B 303 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (12716)
  covalent geometry    : angle       0.72441 (17340)
  hydrogen bonds       : bond        0.04092 (  632)
  hydrogen bonds       : angle       4.57672 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 THR cc_start: 0.9419 (m) cc_final: 0.8968 (p)
REVERT: A  556 LEU cc_start: 0.8751 (mm) cc_final: 0.8336 (mm)
REVERT: A  682 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7490 (ptt)
REVERT: A  697 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.5770 (tmm)
REVERT: A  724 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7296 (t80)
REVERT: A  745 PHE cc_start: 0.8639 (m-10) cc_final: 0.8210 (m-10)
REVERT: A  748 MET cc_start: 0.8578 (mmm) cc_final: 0.7814 (mmt)
REVERT: B   70 LEU cc_start: 0.7870 (tp) cc_final: 0.7487 (tt)
REVERT: B  110 MET cc_start: 0.8519 (mmm) cc_final: 0.8306 (mmm)
REVERT: B  344 LEU cc_start: 0.8634 (tp) cc_final: 0.8249 (pp)
REVERT: B  350 PHE cc_start: 0.7112 (m-10) cc_final: 0.6810 (m-10)
REVERT: B  585 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7551 (mm)
REVERT: B  619 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7374 (tp)
REVERT: B  647 LEU cc_start: 0.8271 (mm) cc_final: 0.7970 (mm)
REVERT: B  714 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7751 (m)
REVERT: B  771 PHE cc_start: 0.7682 (m-80) cc_final: 0.7297 (m-80)
  outliers start: 32
  outliers final: 22
  residues processed: 177
  average time/residue: 0.0917
  time to fit residues: 25.6702
Evaluate side-chains
  182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  520 HIS
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 130 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 143 optimal weight:    7.9990
   chunk 100 optimal weight:    9.9990
   chunk 126 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 135 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
B 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.155820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108252 restraints weight = 21190.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.109135 restraints weight = 15781.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.108978 restraints weight = 13971.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.109133 restraints weight = 13634.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.109285 restraints weight = 12731.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12716  Z= 0.158
  Angle     :  0.729  17.492  17340  Z= 0.339
  Chirality :  0.046   0.392   1982
  Planarity :  0.004   0.060   2190
  Dihedral  :  4.550  22.498   1681
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.35 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.22), residues: 1555
  helix:  1.47 (0.19), residues: 753
  sheet: -1.04 (0.36), residues: 197
  loop : -0.31 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 473 
 TYR   0.015   0.001   TYR A 389 
 PHE   0.033   0.002   PHE B 750 
 TRP   0.013   0.001   TRP B 303 
 HIS   0.004   0.001   HIS A 447 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (12716)
  covalent geometry    : angle       0.72928 (17340)
  hydrogen bonds       : bond        0.04057 (  632)
  hydrogen bonds       : angle       4.56628 ( 1770)

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

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

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3110 Ramachandran restraints generated.
    1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 THR cc_start: 0.9443 (m) cc_final: 0.8997 (p)
REVERT: A  556 LEU cc_start: 0.8755 (mm) cc_final: 0.8534 (mm)
REVERT: A  682 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7444 (ptt)
REVERT: A  697 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5781 (tmm)
REVERT: A  724 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7311 (t80)
REVERT: A  745 PHE cc_start: 0.8671 (m-10) cc_final: 0.8239 (m-10)
REVERT: A  748 MET cc_start: 0.8576 (mmm) cc_final: 0.7821 (mmt)
REVERT: B   70 LEU cc_start: 0.7829 (tp) cc_final: 0.7439 (tt)
REVERT: B  344 LEU cc_start: 0.8461 (tp) cc_final: 0.8127 (pp)
REVERT: B  585 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7540 (mm)
REVERT: B  619 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7379 (tp)
REVERT: B  714 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7742 (m)
REVERT: B  771 PHE cc_start: 0.7805 (m-80) cc_final: 0.7399 (m-80)
  outliers start: 31
  outliers final: 23
  residues processed: 174
  average time/residue: 0.0904
  time to fit residues: 24.8970
Evaluate side-chains
  182 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 153
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  615 TYR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain A residue  708 THR
Chi-restraints excluded: chain A residue  724 TYR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  520 HIS
Chi-restraints excluded: chain B residue  524 TYR
Chi-restraints excluded: chain B residue  577 LEU
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  701 CYS
Chi-restraints excluded: chain B residue  714 THR
Chi-restraints excluded: chain B residue  762 ARG
Chi-restraints excluded: chain B residue  790 VAL
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 145 optimal weight:    4.9990
   chunk 154 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 123 optimal weight:    0.6980
   chunk 105 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   chunk 131 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   chunk 45 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0050
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
B 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.157789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.108560 restraints weight = 21169.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110450 restraints weight = 16790.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.111201 restraints weight = 13111.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.111340 restraints weight = 11839.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.111565 restraints weight = 12096.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12716  Z= 0.116
  Angle     :  0.716  17.851  17340  Z= 0.329
  Chirality :  0.045   0.394   1982
  Planarity :  0.004   0.061   2190
  Dihedral  :  4.385  21.508   1681
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.79 %
    Favored  : 82.26 %
  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:  0.77 (0.22), residues: 1555
  helix:  1.60 (0.19), residues: 753
  sheet: -0.99 (0.36), residues: 197
  loop : -0.25 (0.27), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 506 
 TYR   0.011   0.001   TYR A 389 
 PHE   0.034   0.001   PHE B 750 
 TRP   0.019   0.001   TRP B 303 
 HIS   0.003   0.001   HIS B 646 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12716)
  covalent geometry    : angle       0.71601 (17340)
  hydrogen bonds       : bond        0.03739 (  632)
  hydrogen bonds       : angle       4.50713 ( 1770)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2234.78 seconds
wall clock time: 39 minutes 25.68 seconds (2365.68 seconds total)