Starting phenix.real_space_refine
on Tue Jul 29 00:55:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qm9_4592/07_2025/6qm9_4592.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qm9_4592/07_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_4592/07_2025/6qm9_4592.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qm9_4592/07_2025/6qm9_4592.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qm9_4592/07_2025/6qm9_4592.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qm9_4592/07_2025/6qm9_4592.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.99, per 1000 atoms: 1.10
  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: 3.48
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.10
  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: 4.76

  Time building geometry restraints manager: 3.82 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: 0.04
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:                  0.010
  Normalize map: mean=0, sd=1:             116.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     35.090
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  156.210
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.015   0.002   TRP A 235 
 HIS   0.004   0.001   HIS A 366 
 PHE   0.040   0.002   PHE B 396 
 TYR   0.014   0.001   TYR A  26 
 ARG   0.006   0.001   ARG A 432 

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

*********************** 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  : 1.636 
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: 0.8343 (mt)
REVERT: A  407 TRP cc_start: 0.8506 (m100) cc_final: 0.8159 (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: 0.3921
  time to fit residues: 100.3543
Evaluate side-chains
  123 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 101 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 105 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  79 GLN
A 310 ASN
A 374 GLN
A 378 ASN
A 479 HIS
A 531 ASN
** B  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 GLN
B 310 ASN
B 374 GLN
B 378 ASN
B 479 HIS
B 531 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.117799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.086096 restraints weight = 20774.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.088705 restraints weight = 10591.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.090315 restraints weight = 7371.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  11154  Z= 0.230
  Angle     :  0.657   6.834  15126  Z= 0.352
  Chirality :  0.042   0.173   1660
  Planarity :  0.005   0.037   1920
  Dihedral  :  4.880  18.600   1446
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.82 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.19), residues: 1322
  helix: -1.72 (0.14), residues: 914
  sheet: -1.84 (0.66), residues: 48
  loop : -2.04 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 570 
 HIS   0.003   0.001   HIS A 611 
 PHE   0.020   0.002   PHE A 315 
 TYR   0.016   0.002   TYR A 360 
 ARG   0.008   0.001   ARG B 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04819 (  634)
  hydrogen bonds       : angle       4.54823 ( 1884)
  covalent geometry    : bond        0.00516 (11154)
  covalent geometry    : angle       0.65683 (15126)

*********************** 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
  158 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 GLU cc_start: 0.8427 (pp20) cc_final: 0.8166 (pp20)
REVERT: A  338 ILE cc_start: 0.8763 (mm) cc_final: 0.8535 (mt)
REVERT: B  313 GLU cc_start: 0.8385 (pp20) cc_final: 0.8120 (pp20)
REVERT: B  315 PHE cc_start: 0.9054 (t80) cc_final: 0.8649 (t80)
REVERT: B  338 ILE cc_start: 0.8756 (mm) cc_final: 0.8533 (mt)
REVERT: B  406 PHE cc_start: 0.8254 (t80) cc_final: 0.7712 (t80)
REVERT: B  407 TRP cc_start: 0.8673 (m100) cc_final: 0.8078 (m100)
  outliers start: 23
  outliers final: 20
  residues processed: 145
  average time/residue: 0.2606
  time to fit residues: 55.4126
Evaluate side-chains
  127 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 1.295 
-------------------------------------------------------------------------------
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  441 THR
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  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  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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 102 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 131 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   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  58 HIS
** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 HIS
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.119947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.088174 restraints weight = 20806.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.090810 restraints weight = 10583.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.092435 restraints weight = 7339.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2460

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= 0.138
  Angle     :  0.548   6.891  15126  Z= 0.286
  Chirality :  0.039   0.144   1660
  Planarity :  0.004   0.035   1920
  Dihedral  :  4.467  16.260   1446
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 14.34 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.22), residues: 1322
  helix: -0.36 (0.16), residues: 920
  sheet: -1.64 (0.70), residues: 48
  loop : -1.97 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 235 
 HIS   0.002   0.001   HIS B 611 
 PHE   0.034   0.001   PHE B 205 
 TYR   0.017   0.001   TYR A  26 
 ARG   0.005   0.000   ARG B 424 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  634)
  hydrogen bonds       : angle       4.00711 ( 1884)
  covalent geometry    : bond        0.00309 (11154)
  covalent geometry    : angle       0.54810 (15126)

*********************** 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
  171 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 1.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 GLU cc_start: 0.8409 (pp20) cc_final: 0.8205 (pp20)
REVERT: A  338 ILE cc_start: 0.8777 (mm) cc_final: 0.8509 (mt)
REVERT: A  406 PHE cc_start: 0.7601 (t80) cc_final: 0.7306 (t80)
REVERT: B  313 GLU cc_start: 0.8338 (pp20) cc_final: 0.8093 (pp20)
REVERT: B  315 PHE cc_start: 0.9060 (t80) cc_final: 0.8566 (t80)
REVERT: B  338 ILE cc_start: 0.8780 (mm) cc_final: 0.8528 (mt)
REVERT: B  406 PHE cc_start: 0.8099 (t80) cc_final: 0.7603 (t80)
  outliers start: 36
  outliers final: 27
  residues processed: 152
  average time/residue: 0.2799
  time to fit residues: 63.2076
Evaluate side-chains
  147 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
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  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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 119 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3604 r_free = 0.3604 target = 0.120101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.087684 restraints weight = 20725.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.090391 restraints weight = 10530.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.092092 restraints weight = 7298.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11154  Z= 0.149
  Angle     :  0.551   6.927  15126  Z= 0.279
  Chirality :  0.039   0.142   1660
  Planarity :  0.003   0.034   1920
  Dihedral  :  4.279  14.710   1446
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.23), residues: 1322
  helix:  0.22 (0.17), residues: 922
  sheet: -1.34 (0.73), residues: 48
  loop : -1.80 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 235 
 HIS   0.002   0.001   HIS B 611 
 PHE   0.029   0.001   PHE B 205 
 TYR   0.017   0.001   TYR B  26 
 ARG   0.006   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03645 (  634)
  hydrogen bonds       : angle       3.84456 ( 1884)
  covalent geometry    : bond        0.00338 (11154)
  covalent geometry    : angle       0.55057 (15126)

*********************** 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
  172 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 129
  time to evaluate  : 1.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  313 GLU cc_start: 0.8406 (pp20) cc_final: 0.8179 (pp20)
REVERT: A  338 ILE cc_start: 0.8709 (mm) cc_final: 0.8458 (mt)
REVERT: A  460 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8429 (mm-40)
REVERT: B  313 GLU cc_start: 0.8401 (pp20) cc_final: 0.8164 (pp20)
REVERT: B  315 PHE cc_start: 0.9015 (t80) cc_final: 0.8602 (t80)
REVERT: B  338 ILE cc_start: 0.8719 (mm) cc_final: 0.8460 (mt)
  outliers start: 43
  outliers final: 32
  residues processed: 149
  average time/residue: 0.2522
  time to fit residues: 56.0513
Evaluate side-chains
  156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 2.583 
-------------------------------------------------------------------------------
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  346 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  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  312 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 126 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 92 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3587 r_free = 0.3587 target = 0.118867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.086131 restraints weight = 20762.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.088815 restraints weight = 10682.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.090493 restraints weight = 7456.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.2856

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= 0.197
  Angle     :  0.576   7.053  15126  Z= 0.293
  Chirality :  0.041   0.148   1660
  Planarity :  0.004   0.036   1920
  Dihedral  :  4.251  14.002   1446
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 15.46 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1322
  helix:  0.48 (0.17), residues: 922
  sheet: -1.12 (0.76), residues: 48
  loop : -1.77 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 235 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.035   0.001   PHE A 205 
 TYR   0.018   0.001   TYR A  26 
 ARG   0.007   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03751 (  634)
  hydrogen bonds       : angle       3.87178 ( 1884)
  covalent geometry    : bond        0.00454 (11154)
  covalent geometry    : angle       0.57593 (15126)

*********************** 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
  166 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 121
  time to evaluate  : 1.547 
Fit side-chains
REVERT: A  197 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8212 (mtt90)
REVERT: A  313 GLU cc_start: 0.8433 (pp20) cc_final: 0.8218 (pp20)
REVERT: A  338 ILE cc_start: 0.8688 (mm) cc_final: 0.8443 (mt)
REVERT: A  406 PHE cc_start: 0.8261 (t80) cc_final: 0.7728 (t80)
REVERT: A  460 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8389 (mm-40)
REVERT: B  197 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8186 (mtt90)
REVERT: B  313 GLU cc_start: 0.8488 (pp20) cc_final: 0.8271 (pp20)
REVERT: B  315 PHE cc_start: 0.9029 (t80) cc_final: 0.8580 (t80)
REVERT: B  338 ILE cc_start: 0.8681 (mm) cc_final: 0.8431 (mt)
REVERT: B  406 PHE cc_start: 0.7953 (t80) cc_final: 0.7613 (t80)
  outliers start: 45
  outliers final: 35
  residues processed: 145
  average time/residue: 0.3273
  time to fit residues: 71.8928
Evaluate side-chains
  153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
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  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  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  197 ARG
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0040
   chunk 100 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.8594

-------------------------------------------------------------------------------
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 = 0.3617 r_free = 0.3617 target = 0.120807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.089105 restraints weight = 20759.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.091762 restraints weight = 10678.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.093368 restraints weight = 7478.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3013

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= 0.114
  Angle     :  0.536   7.940  15126  Z= 0.267
  Chirality :  0.039   0.145   1660
  Planarity :  0.003   0.033   1920
  Dihedral  :  4.125  13.293   1446
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.88 %
    Favored  : 78.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.23), residues: 1322
  helix:  0.71 (0.17), residues: 920
  sheet: -0.94 (0.78), residues: 48
  loop : -1.70 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 407 
 HIS   0.002   0.001   HIS A 153 
 PHE   0.039   0.001   PHE B 205 
 TYR   0.017   0.001   TYR B  26 
 ARG   0.007   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (  634)
  hydrogen bonds       : angle       3.68092 ( 1884)
  covalent geometry    : bond        0.00260 (11154)
  covalent geometry    : angle       0.53584 (15126)

*********************** 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
  174 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 137
  time to evaluate  : 1.369 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8291 (tp)
REVERT: A  141 TRP cc_start: 0.8121 (OUTLIER) cc_final: 0.7418 (p90)
REVERT: A  197 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8121 (mtt90)
REVERT: A  338 ILE cc_start: 0.8649 (mm) cc_final: 0.8391 (mt)
REVERT: A  406 PHE cc_start: 0.8130 (t80) cc_final: 0.7581 (t80)
REVERT: A  460 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8362 (mm-40)
REVERT: A  521 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8754 (t60)
REVERT: B  141 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7473 (p90)
REVERT: B  338 ILE cc_start: 0.8642 (mm) cc_final: 0.8387 (mt)
REVERT: B  406 PHE cc_start: 0.7806 (t80) cc_final: 0.7564 (t80)
REVERT: B  521 TRP cc_start: 0.8955 (OUTLIER) cc_final: 0.8749 (t60)
REVERT: B  711 MET cc_start: 0.8407 (tpp) cc_final: 0.8069 (mmt)
  outliers start: 37
  outliers final: 25
  residues processed: 154
  average time/residue: 0.2085
  time to fit residues: 47.8962
Evaluate side-chains
  160 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
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  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  521 TRP
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  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  251 VAL
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 ILE
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  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 63 optimal weight:    0.0060
   chunk 33 optimal weight:    9.9990
   chunk 80 optimal weight:    0.0770
   chunk 117 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   chunk 68 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    1.8160

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.118984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.086881 restraints weight = 20940.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.089420 restraints weight = 10877.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.090994 restraints weight = 7697.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.3076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11154  Z= 0.174
  Angle     :  0.575   9.178  15126  Z= 0.288
  Chirality :  0.040   0.152   1660
  Planarity :  0.004   0.041   1920
  Dihedral  :  4.123  13.126   1446
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 18.13 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1322
  helix:  0.78 (0.17), residues: 924
  sheet: -0.81 (0.80), residues: 48
  loop : -1.62 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 407 
 HIS   0.003   0.001   HIS B 611 
 PHE   0.037   0.001   PHE B 205 
 TYR   0.017   0.001   TYR B  26 
 ARG   0.006   0.000   ARG A  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  634)
  hydrogen bonds       : angle       3.73059 ( 1884)
  covalent geometry    : bond        0.00405 (11154)
  covalent geometry    : angle       0.57477 (15126)

*********************** 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: 41
    poor density    : 124
  time to evaluate  : 1.727 
Fit side-chains
REVERT: A  141 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7220 (p90)
REVERT: A  197 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8138 (mtt90)
REVERT: A  338 ILE cc_start: 0.8671 (mm) cc_final: 0.8414 (mt)
REVERT: A  460 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8355 (mm-40)
REVERT: B  141 TRP cc_start: 0.8183 (OUTLIER) cc_final: 0.7148 (p90)
REVERT: B  197 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8267 (mtt90)
REVERT: B  338 ILE cc_start: 0.8651 (mm) cc_final: 0.8397 (mt)
REVERT: B  406 PHE cc_start: 0.7784 (t80) cc_final: 0.7548 (t80)
  outliers start: 41
  outliers final: 32
  residues processed: 148
  average time/residue: 0.3407
  time to fit residues: 74.4823
Evaluate side-chains
  153 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 117
  time to evaluate  : 2.743 
-------------------------------------------------------------------------------
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  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  580 VAL
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  197 ARG
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  312 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 129 optimal weight:    0.9990
   chunk 132 optimal weight:    0.9980
   chunk 60 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 107 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3627 r_free = 0.3627 target = 0.121545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.088887 restraints weight = 20550.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091630 restraints weight = 10582.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.093329 restraints weight = 7379.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3185

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= 0.118
  Angle     :  0.546   8.103  15126  Z= 0.271
  Chirality :  0.040   0.317   1660
  Planarity :  0.003   0.031   1920
  Dihedral  :  4.076  13.727   1446
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 18.31 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1322
  helix:  0.90 (0.17), residues: 922
  sheet: -0.71 (0.82), residues: 48
  loop : -1.52 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.001   TRP A 407 
 HIS   0.002   0.000   HIS B 611 
 PHE   0.038   0.001   PHE B 205 
 TYR   0.016   0.001   TYR B  26 
 ARG   0.007   0.000   ARG A 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03294 (  634)
  hydrogen bonds       : angle       3.62059 ( 1884)
  covalent geometry    : bond        0.00272 (11154)
  covalent geometry    : angle       0.54568 (15126)

*********************** 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
  174 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 129
  time to evaluate  : 1.619 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8265 (tp)
REVERT: A  141 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.7432 (p90)
REVERT: A  197 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8135 (mtt90)
REVERT: A  338 ILE cc_start: 0.8621 (mm) cc_final: 0.8383 (mt)
REVERT: A  460 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8354 (mm-40)
REVERT: A  521 TRP cc_start: 0.9000 (OUTLIER) cc_final: 0.8787 (t60)
REVERT: B   43 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8257 (tp)
REVERT: B  141 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.7462 (p90)
REVERT: B  197 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8226 (mtt90)
REVERT: B  338 ILE cc_start: 0.8617 (mm) cc_final: 0.8382 (mt)
REVERT: B  521 TRP cc_start: 0.8988 (OUTLIER) cc_final: 0.8765 (t60)
  outliers start: 45
  outliers final: 28
  residues processed: 149
  average time/residue: 0.3596
  time to fit residues: 79.9399
Evaluate side-chains
  156 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 1.381 
-------------------------------------------------------------------------------
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  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  521 TRP
Chi-restraints excluded: chain A residue  530 VAL
Chi-restraints excluded: chain A residue  558 ILE
Chi-restraints excluded: chain A residue  580 VAL
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  197 ARG
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  312 LEU
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    0.1980
   chunk 78 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   chunk 123 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3624 r_free = 0.3624 target = 0.121352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.089708 restraints weight = 20754.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.092362 restraints weight = 10614.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.093962 restraints weight = 7419.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11154  Z= 0.110
  Angle     :  0.553  10.120  15126  Z= 0.273
  Chirality :  0.039   0.146   1660
  Planarity :  0.003   0.030   1920
  Dihedral  :  4.010  14.536   1446
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.57 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1322
  helix:  1.06 (0.17), residues: 926
  sheet: -0.72 (0.83), residues: 48
  loop : -1.39 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 407 
 HIS   0.002   0.000   HIS A 153 
 PHE   0.038   0.001   PHE B 205 
 TYR   0.015   0.001   TYR B  26 
 ARG   0.007   0.000   ARG B 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03217 (  634)
  hydrogen bonds       : angle       3.57102 ( 1884)
  covalent geometry    : bond        0.00247 (11154)
  covalent geometry    : angle       0.55343 (15126)

*********************** 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
  169 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 3.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8192 (tp)
REVERT: A  141 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7536 (p90)
REVERT: A  197 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8158 (mtt180)
REVERT: A  338 ILE cc_start: 0.8666 (mm) cc_final: 0.8436 (mt)
REVERT: A  357 MET cc_start: 0.7610 (ppp) cc_final: 0.6530 (ppp)
REVERT: A  460 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8327 (mm-40)
REVERT: A  510 GLN cc_start: 0.8699 (tt0) cc_final: 0.8376 (tt0)
REVERT: A  521 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8765 (t60)
REVERT: B   43 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8192 (tp)
REVERT: B  141 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7566 (p90)
REVERT: B  338 ILE cc_start: 0.8661 (mm) cc_final: 0.8435 (mt)
REVERT: B  406 PHE cc_start: 0.8218 (t80) cc_final: 0.7653 (t80)
REVERT: B  521 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.8743 (t60)
REVERT: B  711 MET cc_start: 0.8383 (tpp) cc_final: 0.8053 (mmt)
  outliers start: 40
  outliers final: 26
  residues processed: 148
  average time/residue: 0.2888
  time to fit residues: 63.6583
Evaluate side-chains
  151 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 1.664 
-------------------------------------------------------------------------------
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  271 ILE
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  580 VAL
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  312 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 5 optimal weight:    0.0470
   chunk 106 optimal weight:    0.5980
   chunk 33 optimal weight:   10.0000
   chunk 101 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0670
   chunk 108 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.3420

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3600 r_free = 0.3600 target = 0.119810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.088244 restraints weight = 20681.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.090809 restraints weight = 10652.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.092382 restraints weight = 7470.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11154  Z= 0.143
  Angle     :  0.572   8.948  15126  Z= 0.285
  Chirality :  0.040   0.151   1660
  Planarity :  0.003   0.029   1920
  Dihedral  :  3.996  13.604   1446
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.17 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1322
  helix:  1.09 (0.17), residues: 930
  sheet: -0.59 (0.85), residues: 48
  loop : -1.33 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 407 
 HIS   0.002   0.001   HIS A 153 
 PHE   0.036   0.001   PHE B 205 
 TYR   0.015   0.001   TYR B  26 
 ARG   0.007   0.000   ARG B 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  634)
  hydrogen bonds       : angle       3.58919 ( 1884)
  covalent geometry    : bond        0.00331 (11154)
  covalent geometry    : angle       0.57165 (15126)

********************** 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
  157 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7544 (p90)
REVERT: A  197 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8148 (mtt90)
REVERT: A  338 ILE cc_start: 0.8666 (mm) cc_final: 0.8440 (mt)
REVERT: A  357 MET cc_start: 0.7653 (ppp) cc_final: 0.6563 (ppp)
REVERT: A  460 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8332 (mm-40)
REVERT: A  510 GLN cc_start: 0.8784 (tt0) cc_final: 0.8485 (tt0)
REVERT: A  521 TRP cc_start: 0.9020 (OUTLIER) cc_final: 0.8792 (t60)
REVERT: A  638 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7977 (mt-10)
REVERT: B  141 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.7514 (p90)
REVERT: B  338 ILE cc_start: 0.8681 (mm) cc_final: 0.8461 (mt)
REVERT: B  357 MET cc_start: 0.7665 (ppp) cc_final: 0.6559 (ppp)
  outliers start: 36
  outliers final: 30
  residues processed: 139
  average time/residue: 0.1869
  time to fit residues: 39.2543
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  : 1.161 
-------------------------------------------------------------------------------
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  251 VAL
Chi-restraints excluded: chain A residue  271 ILE
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  580 VAL
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  251 VAL
Chi-restraints excluded: chain B residue  260 GLU
Chi-restraints excluded: chain B residue  271 ILE
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 127 optimal weight:    0.7980
   chunk 130 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0870
   chunk 100 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 116 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 123 optimal weight:    7.9990
   overall best weight:    1.5362

-------------------------------------------------------------------------------
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 171 GLN
** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.119773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.087768 restraints weight = 20646.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.090414 restraints weight = 10480.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.092032 restraints weight = 7284.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
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      :  0.004   0.042  11154  Z= 0.155
  Angle     :  0.585   8.452  15126  Z= 0.290
  Chirality :  0.040   0.152   1660
  Planarity :  0.003   0.030   1920
  Dihedral  :  4.024  13.668   1446
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 18.91 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.24), residues: 1322
  helix:  1.10 (0.17), residues: 930
  sheet: -0.52 (0.85), residues: 48
  loop : -1.22 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 407 
 HIS   0.002   0.001   HIS A 153 
 PHE   0.036   0.001   PHE B 205 
 TYR   0.016   0.001   TYR B  26 
 ARG   0.007   0.000   ARG A 710 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  634)
  hydrogen bonds       : angle       3.61483 ( 1884)
  covalent geometry    : bond        0.00358 (11154)
  covalent geometry    : angle       0.58540 (15126)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4549.19 seconds
wall clock time: 88 minutes 37.60 seconds (5317.60 seconds total)