Starting phenix.real_space_refine
on Tue Nov 18 04:06:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qm9_4592/11_2025/6qm9_4592.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     S      40      5.16       5
     C    7068      2.51       5
     N    1818      2.21       5
     O    1948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10878
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5437
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 29, 'TRANS': 643}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.83, per 1000 atoms: 0.44
  Number of scatterers: 10878
  At special positions: 0
  Unit cell: (120.428, 110.308, 110.308, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      4     19.99
     S      40     16.00
     O    1948      8.00
     N    1818      7.00
     C    7068      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: 0.89
  Conformation dependent library (CDL) restraints added in 422.7 milliseconds
  

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2552

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 4 sheets defined
      71.2% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 48
    Processing helix  chain 'A' and resid 72 through 90
      removed outlier: 3.646A  pdb=" N   GLN A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 111 through 124
    Processing helix  chain 'A' and resid 135 through 139
    Processing helix  chain 'A' and resid 152 through 166
    Processing helix  chain 'A' and resid 170 through 198
      removed outlier: 3.693A  pdb=" N   ILE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   GLU A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
      removed outlier: 9.407A  pdb=" N   SER A 184 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   VAL A 185 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   TYR A 188 " --> pdb=" O   SER A 184 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
      removed outlier: 3.599A  pdb=" N   PHE A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 246
      removed outlier: 3.777A  pdb=" N   VAL A 229 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL A 244 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 289
      removed outlier: 3.735A  pdb=" N   ARG A 284 " --> pdb=" O   PRO A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 302
      removed outlier: 3.751A  pdb=" N   ALA A 297 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   VAL A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 317
      removed outlier: 3.534A  pdb=" N   GLU A 313 " --> pdb=" O   CYS A 309 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 359
      removed outlier: 3.813A  pdb=" N   ILE A 338 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      Proline residue:  A 341  - end of helix
      removed outlier: 3.558A  pdb=" N   SER A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 3.543A  pdb=" N   LYS A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 392
      removed outlier: 3.728A  pdb=" N   THR A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 412
      removed outlier: 3.581A  pdb=" N   ALA A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN A 412 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 453
      removed outlier: 3.563A  pdb=" N   VAL A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ALA A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLN A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A 446 " --> pdb=" O   VAL A 442 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   VAL A 453 " --> pdb=" O   PHE A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
      removed outlier: 3.618A  pdb=" N   LYS A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 494
      removed outlier: 4.243A  pdb=" N   PHE A 485 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   THR A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 518
      removed outlier: 3.902A  pdb=" N   GLU A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   MET A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER A 518 " --> pdb=" O   VAL A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 546
      removed outlier: 3.718A  pdb=" N   VAL A 530 " --> pdb=" O   CYS A 526 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL A 534 " --> pdb=" O   VAL A 530 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG A 537 " --> pdb=" O   TRP A 533 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA A 544 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 584
      removed outlier: 3.581A  pdb=" N   ILE A 574 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR A 581 " --> pdb=" O   SER A 577 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER A 584 " --> pdb=" O   VAL A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 627
      removed outlier: 3.697A  pdb=" N   LEU A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA A 609 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 649
      removed outlier: 3.556A  pdb=" N   GLN A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A 634 " --> pdb=" O   PRO A 630 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU A 635 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   GLU A 638 " --> pdb=" O   LYS A 634 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS A 643 " --> pdb=" O   ARG A 639 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 646 " --> pdb=" O   THR A 642 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU A 649 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 682
      removed outlier: 3.825A  pdb=" N   ILE A 670 " --> pdb=" O   HIS A 666 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN A 681 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 696
      removed outlier: 3.922A  pdb=" N   TRP A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN A 696 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 718
      removed outlier: 3.729A  pdb=" N   ALA A 718 " --> pdb=" O   GLN A 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 48
    Processing helix  chain 'B' and resid 72 through 90
      removed outlier: 3.646A  pdb=" N   GLN B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 111 through 124
    Processing helix  chain 'B' and resid 135 through 139
    Processing helix  chain 'B' and resid 152 through 166
    Processing helix  chain 'B' and resid 170 through 198
      removed outlier: 3.693A  pdb=" N   ILE B 174 " --> pdb=" O   GLU B 170 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ILE B 177 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY B 182 " --> pdb=" O   ARG B 178 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   GLU B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
      removed outlier: 9.407A  pdb=" N   SER B 184 " --> pdb=" O   LYS B 180 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   VAL B 185 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA B 186 " --> pdb=" O   GLY B 182 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   TYR B 188 " --> pdb=" O   SER B 184 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 3.599A  pdb=" N   PHE B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 246
      removed outlier: 3.777A  pdb=" N   VAL B 229 " --> pdb=" O   GLY B 225 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   PHE B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL B 240 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   VAL B 244 " --> pdb=" O   VAL B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 289
      removed outlier: 3.735A  pdb=" N   ARG B 284 " --> pdb=" O   PRO B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 302
      removed outlier: 3.751A  pdb=" N   ALA B 297 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL B 300 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 317
      removed outlier: 3.534A  pdb=" N   GLU B 313 " --> pdb=" O   CYS B 309 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE B 315 " --> pdb=" O   SER B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 359
      removed outlier: 3.813A  pdb=" N   ILE B 338 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY B 339 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
      removed outlier: 3.558A  pdb=" N   SER B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 381
      removed outlier: 3.543A  pdb=" N   LYS B 373 " --> pdb=" O   ALA B 369 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   VAL B 376 " --> pdb=" O   GLN B 372 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 392
      removed outlier: 3.729A  pdb=" N   THR B 389 " --> pdb=" O   ALA B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 412
      removed outlier: 3.581A  pdb=" N   ALA B 409 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLN B 412 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 453
      removed outlier: 3.564A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ALA B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLN B 445 " --> pdb=" O   THR B 441 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE B 446 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL B 453 " --> pdb=" O   PHE B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 471
      removed outlier: 3.617A  pdb=" N   LYS B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS B 470 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 494
      removed outlier: 4.243A  pdb=" N   PHE B 485 " --> pdb=" O   GLU B 481 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   THR B 494 " --> pdb=" O   ARG B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 518
      removed outlier: 3.902A  pdb=" N   GLU B 506 " --> pdb=" O   GLY B 502 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET B 507 " --> pdb=" O   ASP B 503 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   SER B 518 " --> pdb=" O   VAL B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 546
      removed outlier: 3.718A  pdb=" N   VAL B 530 " --> pdb=" O   CYS B 526 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL B 534 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG B 537 " --> pdb=" O   TRP B 533 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA B 540 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B 546 " --> pdb=" O   LYS B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 584
      removed outlier: 3.581A  pdb=" N   ILE B 574 " --> pdb=" O   TRP B 570 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER B 577 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   VAL B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR B 581 " --> pdb=" O   SER B 577 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   SER B 584 " --> pdb=" O   VAL B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 627
      removed outlier: 3.697A  pdb=" N   LEU B 602 " --> pdb=" O   LYS B 598 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ALA B 609 " --> pdb=" O   SER B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 649
      removed outlier: 3.556A  pdb=" N   GLN B 633 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS B 634 " --> pdb=" O   PRO B 630 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 635 " --> pdb=" O   GLY B 631 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLU B 638 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS B 643 " --> pdb=" O   ARG B 639 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B 646 " --> pdb=" O   THR B 642 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 682
      removed outlier: 3.825A  pdb=" N   ILE B 670 " --> pdb=" O   HIS B 666 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN B 681 " --> pdb=" O   GLU B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 696
      removed outlier: 3.921A  pdb=" N   TRP B 695 " --> pdb=" O   GLU B 691 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN B 696 " --> pdb=" O   GLU B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 718
      removed outlier: 3.729A  pdb=" N   ALA B 718 " --> pdb=" O   GLN B 714 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268
      removed outlier: 4.038A  pdb=" N   HIS A 265 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 278 " --> pdb=" O   HIS A 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 58
    Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268
      removed outlier: 4.039A  pdb=" N   HIS B 265 " --> pdb=" O   VAL B 278 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL B 278 " --> pdb=" O   HIS B 265 " (cutoff:3.500A)

    634 hydrogen bonds defined for protein.
    1884 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: 1.78

  Time building geometry restraints manager: 1.22 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: 3438
        1.34 -     1.46: 1962
        1.46 -     1.57: 5686
        1.57 -     1.69: 2
        1.69 -     1.81: 66
  Bond restraints: 11154
  Sorted by residual:
  bond pdb=" N   PRO B 126 "
       pdb=" CD  PRO B 126 "
    ideal  model  delta    sigma   weight residual
    1.473  1.613 -0.140 1.40e-02 5.10e+03 1.00e+02
  bond pdb=" N   PRO A 126 "
       pdb=" CD  PRO A 126 "
    ideal  model  delta    sigma   weight residual
    1.473  1.613 -0.140 1.40e-02 5.10e+03 9.93e+01
  bond pdb=" C   LEU A 331 "
       pdb=" N   PRO A 332 "
    ideal  model  delta    sigma   weight residual
    1.336  1.380 -0.045 1.23e-02 6.61e+03 1.33e+01
  bond pdb=" C   LEU B 331 "
       pdb=" N   PRO B 332 "
    ideal  model  delta    sigma   weight residual
    1.336  1.380 -0.045 1.23e-02 6.61e+03 1.33e+01
  bond pdb=" C   SER A 595 "
       pdb=" N   PRO A 596 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.51e+00
  ... (remaining 11149 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 14538
        1.95 -     3.91: 495
        3.91 -     5.86: 71
        5.86 -     7.82: 12
        7.82 -     9.77: 10
  Bond angle restraints: 15126
  Sorted by residual:
  angle pdb=" CA  GLU B  60 "
        pdb=" CB  GLU B  60 "
        pdb=" CG  GLU B  60 "
      ideal   model   delta    sigma   weight residual
     114.10  123.30   -9.20 2.00e+00 2.50e-01 2.11e+01
  angle pdb=" C   VAL B 200 "
        pdb=" N   ILE B 201 "
        pdb=" CA  ILE B 201 "
      ideal   model   delta    sigma   weight residual
     120.33  124.01   -3.68 8.00e-01 1.56e+00 2.11e+01
  angle pdb=" CA  GLU A  60 "
        pdb=" CB  GLU A  60 "
        pdb=" CG  GLU A  60 "
      ideal   model   delta    sigma   weight residual
     114.10  123.26   -9.16 2.00e+00 2.50e-01 2.10e+01
  angle pdb=" C   VAL A 200 "
        pdb=" N   ILE A 201 "
        pdb=" CA  ILE A 201 "
      ideal   model   delta    sigma   weight residual
     120.33  123.97   -3.64 8.00e-01 1.56e+00 2.07e+01
  angle pdb=" C   GLU A 452 "
        pdb=" N   VAL A 453 "
        pdb=" CA  VAL A 453 "
      ideal   model   delta    sigma   weight residual
     123.08  119.17    3.91 1.01e+00 9.80e-01 1.50e+01
  ... (remaining 15121 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 5815
       17.62 -    35.24: 598
       35.24 -    52.86: 119
       52.86 -    70.48: 26
       70.48 -    88.10: 16
  Dihedral angle restraints: 6574
    sinusoidal: 2644
      harmonic: 3930
  Sorted by residual:
  dihedral pdb=" CA  LYS A 140 "
           pdb=" C   LYS A 140 "
           pdb=" N   TRP A 141 "
           pdb=" CA  TRP A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LYS B 140 "
           pdb=" C   LYS B 140 "
           pdb=" N   TRP B 141 "
           pdb=" CA  TRP B 141 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  MET A 516 "
           pdb=" C   MET A 516 "
           pdb=" N   PHE A 517 "
           pdb=" CA  PHE A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.16  -16.84     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 6571 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1166
       0.042 -    0.085: 354
       0.085 -    0.127: 96
       0.127 -    0.169: 38
       0.169 -    0.212: 6
  Chirality restraints: 1660
  Sorted by residual:
  chirality pdb=" CA  THR B 340 "
            pdb=" N   THR B 340 "
            pdb=" C   THR B 340 "
            pdb=" CB  THR B 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  THR A 340 "
            pdb=" N   THR A 340 "
            pdb=" C   THR A 340 "
            pdb=" CB  THR A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CB  VAL B 580 "
            pdb=" CA  VAL B 580 "
            pdb=" CG1 VAL B 580 "
            pdb=" CG2 VAL B 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 1657 not shown)

  Planarity restraints: 1920
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 689 "    0.040 5.00e-02 4.00e+02   5.96e-02 5.69e+00
        pdb=" N   PRO A 690 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 690 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 690 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 689 "   -0.040 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO B 690 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 690 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 690 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 455 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.18e+00
        pdb=" N   PRO A 456 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 456 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 456 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1917 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3179
        2.80 -     3.32: 9918
        3.32 -     3.85: 18042
        3.85 -     4.37: 20520
        4.37 -     4.90: 34868
  Nonbonded interactions: 86527
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 188 "
            pdb=" OD2 ASP B 539 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OH  TYR A 188 "
            pdb=" OD2 ASP A 539 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   SER A 667 "
            pdb=" CG1 ILE A 670 "
     model   vdw
     2.277 3.440
  nonbonded pdb=" O   SER B 667 "
            pdb=" CG1 ILE B 670 "
     model   vdw
     2.277 3.440
  nonbonded pdb=" O   GLY B 572 "
            pdb=" OG  SER B 576 "
     model   vdw
     2.297 3.040
  ... (remaining 86522 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:             0.020
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     13.620
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.140  11154  Z= 0.251
  Angle     :  0.888   9.769  15126  Z= 0.529
  Chirality :  0.047   0.212   1660
  Planarity :  0.006   0.060   1920
  Dihedral  : 15.520  88.097   4022
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  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: -6.09 (0.14), residues: 1322
  helix: -4.39 (0.07), residues: 906
  sheet: -2.25 (0.57), residues: 42
  loop : -2.49 (0.27), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 432 
 TYR   0.014   0.001   TYR A  26 
 PHE   0.040   0.002   PHE B 396 
 TRP   0.015   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 (11154)
  covalent geometry    : angle       0.88795 (15126)
  hydrogen bonds       : bond        0.29457 (  634)
  hydrogen bonds       : angle      10.15330 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A  141 TRP cc_start: 0.7508 (p90) cc_final: 0.7176 (p90)
REVERT: A  313 GLU cc_start: 0.8203 (pp20) cc_final: 0.7983 (pp20)
REVERT: A  338 ILE cc_start: 0.8607 (mm) cc_final: 0.8344 (mt)
REVERT: A  407 TRP cc_start: 0.8506 (m100) cc_final: 0.8163 (m100)
REVERT: A  673 GLU cc_start: 0.8299 (tp30) cc_final: 0.8084 (tp30)
REVERT: A  691 GLU cc_start: 0.7848 (pp20) cc_final: 0.7467 (pm20)
REVERT: B  141 TRP cc_start: 0.7564 (p90) cc_final: 0.7216 (p90)
REVERT: B  313 GLU cc_start: 0.8204 (pp20) cc_final: 0.7986 (pp20)
REVERT: B  315 PHE cc_start: 0.9007 (t80) cc_final: 0.8785 (t80)
REVERT: B  338 ILE cc_start: 0.8598 (mm) cc_final: 0.8357 (mt)
REVERT: B  407 TRP cc_start: 0.8526 (m100) cc_final: 0.7967 (m100)
REVERT: B  673 GLU cc_start: 0.8270 (tp30) cc_final: 0.8024 (tp30)
REVERT: B  691 GLU cc_start: 0.7840 (pp20) cc_final: 0.7515 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1223
  time to fit residues: 30.2025
Evaluate side-chains
  124 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A  79 GLN
A 374 GLN
A 479 HIS
A 531 ASN
B  58 HIS
B  79 GLN
B 374 GLN
B 378 ASN
B 479 HIS
B 531 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.119753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.088429 restraints weight = 20775.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.091073 restraints weight = 10578.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.092740 restraints weight = 7293.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.093490 restraints weight = 5999.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.094044 restraints weight = 5473.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11154  Z= 0.159
  Angle     :  0.606   7.323  15126  Z= 0.322
  Chirality :  0.040   0.164   1660
  Planarity :  0.005   0.038   1920
  Dihedral  :  4.845  18.659   1446
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.30 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.19), residues: 1322
  helix: -1.78 (0.14), residues: 910
  sheet: -1.84 (0.66), residues: 48
  loop : -1.97 (0.29), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 424 
 TYR   0.016   0.002   TYR A 360 
 PHE   0.019   0.001   PHE B 205 
 TRP   0.011   0.001   TRP A 561 
 HIS   0.002   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11154)
  covalent geometry    : angle       0.60596 (15126)
  hydrogen bonds       : bond        0.05106 (  634)
  hydrogen bonds       : angle       4.56626 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 GLU cc_start: 0.8366 (pp20) cc_final: 0.8110 (pp20)
REVERT: A  338 ILE cc_start: 0.8777 (mm) cc_final: 0.8543 (mt)
REVERT: A  691 GLU cc_start: 0.7787 (pp20) cc_final: 0.7551 (pm20)
REVERT: B  313 GLU cc_start: 0.8311 (pp20) cc_final: 0.8067 (pp20)
REVERT: B  315 PHE cc_start: 0.9049 (t80) cc_final: 0.8782 (t80)
REVERT: B  338 ILE cc_start: 0.8767 (mm) cc_final: 0.8540 (mt)
REVERT: B  406 PHE cc_start: 0.8180 (t80) cc_final: 0.7639 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1101
  time to fit residues: 22.9428
Evaluate side-chains
  130 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
A 378 ASN
B 310 ASN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.118414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.085832 restraints weight = 21017.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.088398 restraints weight = 11023.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.089989 restraints weight = 7799.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.090885 restraints weight = 6518.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.091170 restraints weight = 5945.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  11154  Z= 0.217
  Angle     :  0.603   7.064  15126  Z= 0.317
  Chirality :  0.041   0.150   1660
  Planarity :  0.004   0.044   1920
  Dihedral  :  4.532  16.142   1446
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.08 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.22), residues: 1322
  helix: -0.38 (0.16), residues: 920
  sheet: -1.61 (0.70), residues: 48
  loop : -1.97 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 424 
 TYR   0.017   0.002   TYR A  26 
 PHE   0.032   0.002   PHE A 205 
 TRP   0.013   0.001   TRP A 235 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 (11154)
  covalent geometry    : angle       0.60320 (15126)
  hydrogen bonds       : bond        0.04211 (  634)
  hydrogen bonds       : angle       4.12831 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 ILE cc_start: 0.8796 (mm) cc_final: 0.8543 (mt)
REVERT: A  406 PHE cc_start: 0.7676 (t80) cc_final: 0.7346 (t80)
REVERT: B  313 GLU cc_start: 0.8371 (pp20) cc_final: 0.8116 (pp20)
REVERT: B  315 PHE cc_start: 0.9070 (t80) cc_final: 0.8582 (t80)
REVERT: B  338 ILE cc_start: 0.8814 (mm) cc_final: 0.8547 (mt)
REVERT: B  406 PHE cc_start: 0.8112 (t80) cc_final: 0.7625 (t80)
  outliers start: 40
  outliers final: 31
  residues processed: 141
  average time/residue: 0.0923
  time to fit residues: 19.7521
Evaluate side-chains
  141 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 125 optimal weight:    3.9990
   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 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.119279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.087600 restraints weight = 20803.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.090198 restraints weight = 10604.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.091832 restraints weight = 7355.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.092721 restraints weight = 6096.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.092722 restraints weight = 5549.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11154  Z= 0.141
  Angle     :  0.545   7.122  15126  Z= 0.277
  Chirality :  0.039   0.142   1660
  Planarity :  0.003   0.034   1920
  Dihedral  :  4.321  14.304   1446
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.72 %
    Favored  : 80.92 %
  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: -0.61 (0.23), residues: 1322
  helix:  0.24 (0.17), residues: 920
  sheet: -1.30 (0.74), residues: 48
  loop : -1.79 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.018   0.001   TYR A  26 
 PHE   0.029   0.001   PHE B 205 
 TRP   0.014   0.001   TRP B 235 
 HIS   0.002   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (11154)
  covalent geometry    : angle       0.54523 (15126)
  hydrogen bonds       : bond        0.03639 (  634)
  hydrogen bonds       : angle       3.85655 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 135
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 ILE cc_start: 0.8724 (mm) cc_final: 0.8464 (mt)
REVERT: A  406 PHE cc_start: 0.7510 (t80) cc_final: 0.7309 (t80)
REVERT: A  460 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8422 (mm-40)
REVERT: B  313 GLU cc_start: 0.8329 (pp20) cc_final: 0.8088 (pp20)
REVERT: B  338 ILE cc_start: 0.8741 (mm) cc_final: 0.8488 (mt)
REVERT: B  460 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8420 (mm-40)
  outliers start: 39
  outliers final: 26
  residues processed: 155
  average time/residue: 0.0981
  time to fit residues: 22.5695
Evaluate side-chains
  153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0980
   chunk 76 optimal weight:    0.0570
   chunk 69 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   chunk 129 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.5902

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.118912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.087218 restraints weight = 20738.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.089815 restraints weight = 10735.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.091384 restraints weight = 7521.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.092273 restraints weight = 6272.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.092569 restraints weight = 5714.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11154  Z= 0.158
  Angle     :  0.554   6.938  15126  Z= 0.281
  Chirality :  0.040   0.144   1660
  Planarity :  0.003   0.030   1920
  Dihedral  :  4.219  14.058   1446
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.46 %
    Favored  : 81.09 %
  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: -0.26 (0.23), residues: 1322
  helix:  0.50 (0.17), residues: 922
  sheet: -1.09 (0.76), residues: 48
  loop : -1.69 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  82 
 TYR   0.017   0.001   TYR A  26 
 PHE   0.026   0.001   PHE B 205 
 TRP   0.013   0.001   TRP A 235 
 HIS   0.002   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11154)
  covalent geometry    : angle       0.55369 (15126)
  hydrogen bonds       : bond        0.03650 (  634)
  hydrogen bonds       : angle       3.82043 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 132
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  141 TRP cc_start: 0.8173 (OUTLIER) cc_final: 0.7167 (p90)
REVERT: A  338 ILE cc_start: 0.8717 (mm) cc_final: 0.8464 (mt)
REVERT: A  460 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8382 (mm-40)
REVERT: B  141 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7242 (p90)
REVERT: B  313 GLU cc_start: 0.8324 (pp20) cc_final: 0.8100 (pp20)
REVERT: B  315 PHE cc_start: 0.8847 (t80) cc_final: 0.8641 (t80)
REVERT: B  338 ILE cc_start: 0.8734 (mm) cc_final: 0.8468 (mt)
REVERT: B  406 PHE cc_start: 0.7835 (t80) cc_final: 0.7570 (t80)
REVERT: B  460 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8382 (mm-40)
  outliers start: 40
  outliers final: 30
  residues processed: 150
  average time/residue: 0.0963
  time to fit residues: 21.4214
Evaluate side-chains
  154 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 128 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 100 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 92 optimal weight:    8.9990
   chunk 124 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.117610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.085530 restraints weight = 20782.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.088047 restraints weight = 10913.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.089636 restraints weight = 7677.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.090421 restraints weight = 6413.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.090634 restraints weight = 5879.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11154  Z= 0.193
  Angle     :  0.582   8.966  15126  Z= 0.294
  Chirality :  0.041   0.150   1660
  Planarity :  0.004   0.031   1920
  Dihedral  :  4.219  14.145   1446
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.18 %
    Favored  : 79.02 %
  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: -0.08 (0.23), residues: 1322
  helix:  0.66 (0.17), residues: 922
  sheet: -0.99 (0.79), residues: 48
  loop : -1.67 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 197 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.037   0.001   PHE A 205 
 TRP   0.030   0.002   TRP A 407 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11154)
  covalent geometry    : angle       0.58160 (15126)
  hydrogen bonds       : bond        0.03714 (  634)
  hydrogen bonds       : angle       3.85722 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 114
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  141 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.6988 (p90)
REVERT: A  338 ILE cc_start: 0.8716 (mm) cc_final: 0.8472 (mt)
REVERT: A  424 ARG cc_start: 0.8715 (mtm180) cc_final: 0.8465 (ptt90)
REVERT: A  460 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8374 (mm-40)
REVERT: B  141 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.6965 (p90)
REVERT: B  338 ILE cc_start: 0.8728 (mm) cc_final: 0.8487 (mt)
REVERT: B  406 PHE cc_start: 0.7881 (t80) cc_final: 0.7622 (t80)
REVERT: B  460 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8364 (mm-40)
  outliers start: 44
  outliers final: 35
  residues processed: 138
  average time/residue: 0.0949
  time to fit residues: 19.8880
Evaluate side-chains
  149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 112
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  441 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  441 THR
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 123 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 78 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.120518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.087975 restraints weight = 20678.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.090736 restraints weight = 10487.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.092421 restraints weight = 7293.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.093385 restraints weight = 6055.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.093662 restraints weight = 5502.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11154  Z= 0.135
  Angle     :  0.551   7.866  15126  Z= 0.275
  Chirality :  0.040   0.215   1660
  Planarity :  0.003   0.030   1920
  Dihedral  :  4.172  14.155   1446
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.74 %
    Favored  : 78.07 %
  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:  0.08 (0.23), residues: 1322
  helix:  0.77 (0.17), residues: 920
  sheet: -0.86 (0.81), residues: 48
  loop : -1.62 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  82 
 TYR   0.017   0.001   TYR B  26 
 PHE   0.035   0.001   PHE A 205 
 TRP   0.059   0.002   TRP A 407 
 HIS   0.002   0.001   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11154)
  covalent geometry    : angle       0.55127 (15126)
  hydrogen bonds       : bond        0.03459 (  634)
  hydrogen bonds       : angle       3.74315 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 128
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7146 (p90)
REVERT: A  338 ILE cc_start: 0.8633 (mm) cc_final: 0.8387 (mt)
REVERT: A  460 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8372 (mm-40)
REVERT: A  521 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8732 (t60)
REVERT: B  141 TRP cc_start: 0.8407 (OUTLIER) cc_final: 0.7082 (p90)
REVERT: B  338 ILE cc_start: 0.8643 (mm) cc_final: 0.8397 (mt)
REVERT: B  406 PHE cc_start: 0.7642 (t80) cc_final: 0.7424 (t80)
REVERT: B  407 TRP cc_start: 0.8560 (m100) cc_final: 0.8294 (m100)
REVERT: B  460 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8363 (mm-40)
REVERT: B  521 TRP cc_start: 0.8980 (OUTLIER) cc_final: 0.8720 (t60)
  outliers start: 37
  outliers final: 27
  residues processed: 148
  average time/residue: 0.0917
  time to fit residues: 20.5367
Evaluate side-chains
  156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  521 TRP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  521 TRP
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 128 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 127 optimal weight:    2.9990
   chunk 114 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.9764

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.118483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.086322 restraints weight = 20704.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.088942 restraints weight = 10502.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.090590 restraints weight = 7289.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.091377 restraints weight = 6048.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.091719 restraints weight = 5542.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11154  Z= 0.184
  Angle     :  0.579   8.103  15126  Z= 0.292
  Chirality :  0.041   0.186   1660
  Planarity :  0.004   0.030   1920
  Dihedral  :  4.203  13.771   1446
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.26 %
    Favored  : 77.37 %
  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:  0.13 (0.23), residues: 1322
  helix:  0.79 (0.17), residues: 924
  sheet: -0.79 (0.83), residues: 48
  loop : -1.54 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 710 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.041   0.001   PHE B 205 
 TRP   0.041   0.002   TRP A 407 
 HIS   0.003   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (11154)
  covalent geometry    : angle       0.57933 (15126)
  hydrogen bonds       : bond        0.03645 (  634)
  hydrogen bonds       : angle       3.80587 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 122
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7055 (p90)
REVERT: A  197 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8193 (mtt90)
REVERT: A  338 ILE cc_start: 0.8649 (mm) cc_final: 0.8398 (mt)
REVERT: A  460 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8356 (mm-40)
REVERT: B  141 TRP cc_start: 0.8506 (OUTLIER) cc_final: 0.7059 (p90)
REVERT: B  338 ILE cc_start: 0.8667 (mm) cc_final: 0.8423 (mt)
REVERT: B  460 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8362 (mm-40)
  outliers start: 39
  outliers final: 31
  residues processed: 142
  average time/residue: 0.0991
  time to fit residues: 20.8244
Evaluate side-chains
  151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  509 MET
Chi-restraints excluded: chain B residue  530 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 120 optimal weight:    0.2980
   chunk 4 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 125 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0770
   chunk 18 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.123237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.090880 restraints weight = 20589.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.093524 restraints weight = 10689.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.095144 restraints weight = 7511.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.095857 restraints weight = 6256.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.096320 restraints weight = 5741.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11154  Z= 0.104
  Angle     :  0.547   8.245  15126  Z= 0.271
  Chirality :  0.038   0.146   1660
  Planarity :  0.003   0.031   1920
  Dihedral  :  4.071  13.447   1446
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.43 %
    Favored  : 77.37 %
  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:  0.36 (0.23), residues: 1322
  helix:  0.97 (0.17), residues: 922
  sheet: -0.68 (0.83), residues: 48
  loop : -1.48 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.042   0.001   PHE B 205 
 TRP   0.054   0.001   TRP A 407 
 HIS   0.002   0.000   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (11154)
  covalent geometry    : angle       0.54719 (15126)
  hydrogen bonds       : bond        0.03253 (  634)
  hydrogen bonds       : angle       3.60467 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 140
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8210 (tp)
REVERT: A  141 TRP cc_start: 0.8358 (OUTLIER) cc_final: 0.7421 (p90)
REVERT: A  197 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (mtt90)
REVERT: A  338 ILE cc_start: 0.8658 (mm) cc_final: 0.8425 (mt)
REVERT: A  460 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8320 (mm-40)
REVERT: A  521 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.8745 (t60)
REVERT: B   43 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8208 (tp)
REVERT: B  141 TRP cc_start: 0.8370 (OUTLIER) cc_final: 0.7371 (p90)
REVERT: B  338 ILE cc_start: 0.8668 (mm) cc_final: 0.8439 (mt)
REVERT: B  460 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8331 (mm-40)
  outliers start: 37
  outliers final: 26
  residues processed: 157
  average time/residue: 0.0975
  time to fit residues: 22.9223
Evaluate side-chains
  160 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  521 TRP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  122 MET
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  507 MET
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 132 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 83 optimal weight:    0.7980
   overall best weight:    1.4382

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 510 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.119771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.088170 restraints weight = 20596.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.090710 restraints weight = 10769.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.092268 restraints weight = 7604.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093131 restraints weight = 6354.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.093172 restraints weight = 5799.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11154  Z= 0.150
  Angle     :  0.584   9.035  15126  Z= 0.289
  Chirality :  0.040   0.154   1660
  Planarity :  0.003   0.030   1920
  Dihedral  :  4.025  13.319   1446
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.52 %
    Favored  : 77.55 %
  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:  0.45 (0.23), residues: 1322
  helix:  1.02 (0.17), residues: 924
  sheet: -0.68 (0.84), residues: 48
  loop : -1.38 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 710 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.039   0.001   PHE B 205 
 TRP   0.047   0.001   TRP A 407 
 HIS   0.002   0.001   HIS B 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (11154)
  covalent geometry    : angle       0.58404 (15126)
  hydrogen bonds       : bond        0.03391 (  634)
  hydrogen bonds       : angle       3.64950 ( 1884)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 TRP cc_start: 0.8389 (OUTLIER) cc_final: 0.7335 (p90)
REVERT: A  197 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8137 (mtt90)
REVERT: A  338 ILE cc_start: 0.8678 (mm) cc_final: 0.8447 (mt)
REVERT: A  357 MET cc_start: 0.7705 (ppp) cc_final: 0.6587 (ppp)
REVERT: A  460 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8308 (mm-40)
REVERT: A  521 TRP cc_start: 0.9016 (OUTLIER) cc_final: 0.8766 (t60)
REVERT: B  141 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7274 (p90)
REVERT: B  338 ILE cc_start: 0.8700 (mm) cc_final: 0.8468 (mt)
REVERT: B  357 MET cc_start: 0.7701 (ppp) cc_final: 0.6581 (ppp)
REVERT: B  460 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8313 (mm-40)
  outliers start: 34
  outliers final: 25
  residues processed: 140
  average time/residue: 0.0906
  time to fit residues: 19.1140
Evaluate side-chains
  149 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   52 LEU
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  141 TRP
Chi-restraints excluded: chain A residue  197 ARG
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  453 VAL
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  521 TRP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  603 LEU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  135 THR
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  334 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  453 VAL
Chi-restraints excluded: chain B residue  500 VAL
Chi-restraints excluded: chain B residue  558 ILE
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  647 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 103 optimal weight:    0.6980
   chunk 98 optimal weight:    0.5980
   chunk 110 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    0.8980
   chunk 133 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.089754 restraints weight = 20569.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.092443 restraints weight = 10450.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.094137 restraints weight = 7195.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.095065 restraints weight = 5951.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.095065 restraints weight = 5395.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11154  Z= 0.111
  Angle     :  0.566   9.045  15126  Z= 0.278
  Chirality :  0.039   0.147   1660
  Planarity :  0.003   0.031   1920
  Dihedral  :  3.979  13.435   1446
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.21 %
    Favored  : 77.12 %
  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:  0.60 (0.23), residues: 1322
  helix:  1.11 (0.17), residues: 926
  sheet: -0.60 (0.84), residues: 48
  loop : -1.29 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 710 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.040   0.001   PHE B 205 
 TRP   0.037   0.001   TRP A 407 
 HIS   0.002   0.000   HIS A 611 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (11154)
  covalent geometry    : angle       0.56591 (15126)
  hydrogen bonds       : bond        0.03195 (  634)
  hydrogen bonds       : angle       3.55351 ( 1884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1726.47 seconds
wall clock time: 30 minutes 40.32 seconds (1840.32 seconds total)