Starting phenix.real_space_refine
on Wed Mar  4 21:41:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yum_34108/03_2026/7yum_34108.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C   10480      2.51       5
     N    2904      2.21       5
     O    3132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16576
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
    Chain: "B"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
    Chain: "C"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
    Chain: "D"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
  Time building chain proxies: 3.62, per 1000 atoms: 0.22
  Number of scatterers: 16576
  At special positions: 0
  Unit cell: (118.08, 109.88, 143.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    3132      8.00
     N    2904      7.00
     C   10480      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: 1.19
  Conformation dependent library (CDL) restraints added in 712.0 milliseconds
  

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3904

  Finding SS restraints...
    Secondary structure from input PDB file:
      87 helices and 18 sheets defined
      44.6% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 245 through 255
      removed outlier: 4.145A  pdb=" N   LYS A 251 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU A 254 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 273
      removed outlier: 4.254A  pdb=" N   ARG A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 296
      removed outlier: 3.770A  pdb=" N   VAL A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 315
    Processing helix  chain 'A' and resid 316 through 318
      No H-bonds generated for 'chain 'A' and resid 316 through 318'
    Processing helix  chain 'A' and resid 324 through 336
    Processing helix  chain 'A' and resid 360 through 373
    Processing helix  chain 'A' and resid 403 through 411
      removed outlier: 3.756A  pdb=" N   HIS A 407 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 444
      removed outlier: 3.529A  pdb=" N   ALA A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 451
      removed outlier: 3.566A  pdb=" N   THR A 450 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   PHE A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 447 through 451'
    Processing helix  chain 'A' and resid 478 through 482
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 505 through 514
      removed outlier: 3.672A  pdb=" N   LYS A 509 " --> pdb=" O   TYR A 505 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER A 514 " --> pdb=" O   GLN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 534
    Processing helix  chain 'A' and resid 540 through 560
      removed outlier: 3.670A  pdb=" N   GLU A 560 " --> pdb=" O   LYS A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 578
      removed outlier: 3.733A  pdb=" N   TYR A 577 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 647
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 717 through 728
      removed outlier: 3.980A  pdb=" N   LYS A 721 " --> pdb=" O   GLY A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 761 through 770
      removed outlier: 3.792A  pdb=" N   VAL A 765 " --> pdb=" O   ASP A 761 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LEU A 770 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 256
    Processing helix  chain 'B' and resid 259 through 271
    Processing helix  chain 'B' and resid 283 through 296
      removed outlier: 3.847A  pdb=" N   VAL B 296 " --> pdb=" O   TRP B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 316
    Processing helix  chain 'B' and resid 325 through 339
      removed outlier: 4.034A  pdb=" N   ILE B 329 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
      removed outlier: 3.660A  pdb=" N   ASN B 373 " --> pdb=" O   ALA B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 403 through 412
      removed outlier: 3.678A  pdb=" N   VAL B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 444
      removed outlier: 4.122A  pdb=" N   ALA B 438 " --> pdb=" O   ASP B 434 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 451
      removed outlier: 3.721A  pdb=" N   THR B 450 " --> pdb=" O   GLN B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 506
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'B' and resid 523 through 535
      removed outlier: 3.636A  pdb=" N   ILE B 527 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   THR B 535 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 560
    Processing helix  chain 'B' and resid 573 through 579
      removed outlier: 3.651A  pdb=" N   TYR B 577 " --> pdb=" O   ASP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 647
      removed outlier: 3.771A  pdb=" N   LYS B 634 " --> pdb=" O   GLY B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 652
      removed outlier: 3.749A  pdb=" N   GLY B 652 " --> pdb=" O   GLN B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 693
    Processing helix  chain 'B' and resid 717 through 728
      removed outlier: 4.100A  pdb=" N   LYS B 721 " --> pdb=" O   GLY B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 740
      No H-bonds generated for 'chain 'B' and resid 738 through 740'
    Processing helix  chain 'B' and resid 742 through 746
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.715A  pdb=" N   LEU B 751 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 769
      removed outlier: 3.714A  pdb=" N   VAL B 765 " --> pdb=" O   ASP B 761 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 256
    Processing helix  chain 'C' and resid 259 through 269
    Processing helix  chain 'C' and resid 281 through 295
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 316 through 318
      No H-bonds generated for 'chain 'C' and resid 316 through 318'
    Processing helix  chain 'C' and resid 324 through 338
      removed outlier: 3.558A  pdb=" N   ARG C 328 " --> pdb=" O   ASP C 324 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU C 338 " --> pdb=" O   ALA C 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 372
    Processing helix  chain 'C' and resid 403 through 412
    Processing helix  chain 'C' and resid 423 through 427
      removed outlier: 4.073A  pdb=" N   MET C 427 " --> pdb=" O   ILE C 424 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 435 through 444
      removed outlier: 3.958A  pdb=" N   VAL C 442 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ASP C 444 " --> pdb=" O   LEU C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 478 through 482
      removed outlier: 3.548A  pdb=" N   LEU C 482 " --> pdb=" O   ARG C 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 515
      removed outlier: 3.549A  pdb=" N   TYR C 505 " --> pdb=" O   ILE C 501 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   TRP C 507 " --> pdb=" O   ARG C 503 " (cutoff:3.500A)
      Proline residue:  C 508  - end of helix
    Processing helix  chain 'C' and resid 523 through 534
      removed outlier: 3.662A  pdb=" N   ILE C 527 " --> pdb=" O   THR C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 540 through 560
      removed outlier: 3.514A  pdb=" N   GLU C 560 " --> pdb=" O   LYS C 556 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 573 through 579
      removed outlier: 3.662A  pdb=" N   TYR C 577 " --> pdb=" O   ASP C 573 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 630 through 647
      removed outlier: 3.652A  pdb=" N   LYS C 634 " --> pdb=" O   GLY C 630 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 679 through 693
    Processing helix  chain 'C' and resid 717 through 728
    Processing helix  chain 'C' and resid 747 through 752
    Processing helix  chain 'C' and resid 761 through 770
      removed outlier: 3.526A  pdb=" N   VAL C 765 " --> pdb=" O   ASP C 761 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU C 770 " --> pdb=" O   LEU C 766 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 255
      removed outlier: 3.832A  pdb=" N   LYS D 252 " --> pdb=" O   ALA D 248 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ILE D 253 " --> pdb=" O   LEU D 249 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLU D 254 " --> pdb=" O   ARG D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 273
    Processing helix  chain 'D' and resid 283 through 296
    Processing helix  chain 'D' and resid 307 through 316
    Processing helix  chain 'D' and resid 324 through 337
      removed outlier: 4.206A  pdb=" N   ARG D 328 " --> pdb=" O   ASP D 324 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 360 through 372
    Processing helix  chain 'D' and resid 386 through 390
      removed outlier: 3.639A  pdb=" N   ILE D 390 " --> pdb=" O   GLU D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 411
    Processing helix  chain 'D' and resid 435 through 444
      removed outlier: 3.822A  pdb=" N   MET D 439 " --> pdb=" O   PRO D 435 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 3.711A  pdb=" N   THR D 476 " --> pdb=" O   THR D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 478 through 482
    Processing helix  chain 'D' and resid 494 through 505
    Processing helix  chain 'D' and resid 505 through 514
      removed outlier: 3.740A  pdb=" N   LYS D 509 " --> pdb=" O   TYR D 505 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG D 512 " --> pdb=" O   PRO D 508 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 523 through 535
      removed outlier: 3.914A  pdb=" N   ILE D 527 " --> pdb=" O   THR D 523 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   THR D 535 " --> pdb=" O   ILE D 531 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 540 through 560
      removed outlier: 3.527A  pdb=" N   GLU D 560 " --> pdb=" O   LYS D 556 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 573 through 578
    Processing helix  chain 'D' and resid 630 through 647
      removed outlier: 3.965A  pdb=" N   LYS D 634 " --> pdb=" O   GLY D 630 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   SER D 636 " --> pdb=" O   VAL D 632 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 648 through 652
    Processing helix  chain 'D' and resid 679 through 691
    Processing helix  chain 'D' and resid 717 through 729
    Processing helix  chain 'D' and resid 738 through 745
      removed outlier: 4.216A  pdb=" N   ALA D 741 " --> pdb=" O   ASP D 738 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLU D 744 " --> pdb=" O   ALA D 741 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 747 through 754
      removed outlier: 3.912A  pdb=" N   LEU D 751 " --> pdb=" O   PRO D 747 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 762 through 769
    Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 354
      removed outlier: 6.014A  pdb=" N   VAL A 352 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 422
      removed outlier: 3.504A  pdb=" N   ILE A 468 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522
      removed outlier: 6.405A  pdb=" N   GLU A 521 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 603
      removed outlier: 6.736A  pdb=" N   SER A 624 " --> pdb=" O   VAL A 665 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 702
      removed outlier: 6.751A  pdb=" N   ILE A 733 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL A 759 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   LEU A 735 " --> pdb=" O   VAL A 759 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 380
      removed outlier: 6.384A  pdb=" N   ILE B 379 " --> pdb=" O   ASP B 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603
      removed outlier: 3.703A  pdb=" N   THR B 603 " --> pdb=" O   GLY B 606 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 732 through 736
      removed outlier: 6.744A  pdb=" N   ILE B 733 " --> pdb=" O   LYS B 757 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   VAL B 759 " --> pdb=" O   ILE B 733 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   LEU B 735 " --> pdb=" O   VAL B 759 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354
    Processing sheet with id=AB1, first strand: chain 'C' and resid 418 through 421
      removed outlier: 3.604A  pdb=" N   ILE C 468 " --> pdb=" O   ILE C 419 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522
      removed outlier: 6.302A  pdb=" N   GLU C 521 " --> pdb=" O   ILE C 569 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 601
      removed outlier: 6.186A  pdb=" N   SER C 624 " --> pdb=" O   VAL C 665 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702
      removed outlier: 6.986A  pdb=" N   ALA C 701 " --> pdb=" O   VAL C 734 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'D' and resid 353 through 354
    Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 380
      removed outlier: 6.227A  pdb=" N   HIS D 377 " --> pdb=" O   LEU D 420 " (cutoff:3.500A)
      removed outlier: 7.221A  pdb=" N   ASP D 422 " --> pdb=" O   HIS D 377 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   ILE D 379 " --> pdb=" O   ASP D 422 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 596 through 603
      removed outlier: 5.537A  pdb=" N   LYS D 622 " --> pdb=" O   LEU D 663 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   VAL D 665 " --> pdb=" O   LYS D 622 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   SER D 624 " --> pdb=" O   VAL D 665 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 700 through 702
      removed outlier: 6.426A  pdb=" N   ALA D 701 " --> pdb=" O   VAL D 734 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ILE D 733 " --> pdb=" O   LYS D 757 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   VAL D 759 " --> pdb=" O   ILE D 733 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   LEU D 735 " --> pdb=" O   VAL D 759 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'D' and resid 705 through 707
      removed outlier: 3.759A  pdb=" N   GLU D 705 " --> pdb=" O   MET D 713 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1818 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: 3.20

  Time building geometry restraints manager: 1.54 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: 5284
        1.34 -     1.45: 2577
        1.45 -     1.57: 8903
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 16884
  Sorted by residual:
  bond pdb=" C   ILE B 419 "
       pdb=" N   LEU B 420 "
    ideal  model  delta    sigma   weight residual
    1.331  1.295  0.036 1.40e-02 5.10e+03 6.73e+00
  bond pdb=" CG  LEU B 769 "
       pdb=" CD1 LEU B 769 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.52e+00
  bond pdb=" CG  LEU B 723 "
       pdb=" CD1 LEU B 723 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.43e+00
  bond pdb=" CB  GLN C 499 "
       pdb=" CG  GLN C 499 "
    ideal  model  delta    sigma   weight residual
    1.520  1.445  0.075 3.00e-02 1.11e+03 6.20e+00
  bond pdb=" CG1 ILE B 468 "
       pdb=" CD1 ILE B 468 "
    ideal  model  delta    sigma   weight residual
    1.513  1.420  0.093 3.90e-02 6.57e+02 5.69e+00
  ... (remaining 16879 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.51: 22365
        3.51 -     7.02: 461
        7.02 -    10.52: 51
       10.52 -    14.03: 5
       14.03 -    17.54: 2
  Bond angle restraints: 22884
  Sorted by residual:
  angle pdb=" N   GLY B 539 "
        pdb=" CA  GLY B 539 "
        pdb=" C   GLY B 539 "
      ideal   model   delta    sigma   weight residual
     111.21  118.38   -7.17 1.04e+00 9.25e-01 4.76e+01
  angle pdb=" C   ALA D 400 "
        pdb=" N   MET D 401 "
        pdb=" CA  MET D 401 "
      ideal   model   delta    sigma   weight residual
     120.97  138.51  -17.54 2.84e+00 1.24e-01 3.81e+01
  angle pdb=" C   GLY B 321 "
        pdb=" N   LEU B 322 "
        pdb=" CA  LEU B 322 "
      ideal   model   delta    sigma   weight residual
     121.54  131.70  -10.16 1.91e+00 2.74e-01 2.83e+01
  angle pdb=" C   MET A 698 "
        pdb=" N   ASP A 699 "
        pdb=" CA  ASP A 699 "
      ideal   model   delta    sigma   weight residual
     122.08  129.85   -7.77 1.47e+00 4.63e-01 2.80e+01
  angle pdb=" N   ILE B 468 "
        pdb=" CA  ILE B 468 "
        pdb=" C   ILE B 468 "
      ideal   model   delta    sigma   weight residual
     109.34   99.73    9.61 2.08e+00 2.31e-01 2.13e+01
  ... (remaining 22879 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.15: 9612
       15.15 -    30.31: 627
       30.31 -    45.46: 120
       45.46 -    60.62: 9
       60.62 -    75.77: 20
  Dihedral angle restraints: 10388
    sinusoidal: 4300
      harmonic: 6088
  Sorted by residual:
  dihedral pdb=" CA  GLU D 591 "
           pdb=" C   GLU D 591 "
           pdb=" N   PRO D 592 "
           pdb=" CA  PRO D 592 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -132.24  -47.76     0      5.00e+00 4.00e-02 9.12e+01
  dihedral pdb=" CA  PRO B 673 "
           pdb=" C   PRO B 673 "
           pdb=" N   LYS B 674 "
           pdb=" CA  LYS B 674 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.02  -41.98     0      5.00e+00 4.00e-02 7.05e+01
  dihedral pdb=" CA  LYS B 347 "
           pdb=" C   LYS B 347 "
           pdb=" N   ALA B 348 "
           pdb=" CA  ALA B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.73   39.27     0      5.00e+00 4.00e-02 6.17e+01
  ... (remaining 10385 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 2058
       0.080 -    0.160: 485
       0.160 -    0.240: 52
       0.240 -    0.320: 6
       0.320 -    0.400: 3
  Chirality restraints: 2604
  Sorted by residual:
  chirality pdb=" CB  ILE C 379 "
            pdb=" CA  ILE C 379 "
            pdb=" CG1 ILE C 379 "
            pdb=" CG2 ILE C 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.00e+00
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" CG  LEU C 462 "
            pdb=" CB  LEU C 462 "
            pdb=" CD1 LEU C 462 "
            pdb=" CD2 LEU C 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.57e+00
  ... (remaining 2601 not shown)

  Planarity restraints: 2972
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 434 "   -0.051 5.00e-02 4.00e+02   7.72e-02 9.53e+00
        pdb=" N   PRO D 435 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO D 435 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO D 435 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 773 "    0.049 5.00e-02 4.00e+02   7.38e-02 8.70e+00
        pdb=" N   PRO A 774 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 774 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 774 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 356 "   -0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO C 357 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO C 357 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 357 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 2969 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2181
        2.75 -     3.29: 16004
        3.29 -     3.82: 27292
        3.82 -     4.36: 31640
        4.36 -     4.90: 53127
  Nonbonded interactions: 130244
  Sorted by model distance:
  nonbonded pdb=" O   LYS C 587 "
            pdb=" OG1 THR C 590 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OG1 THR D 603 "
            pdb=" O   GLY D 606 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR A 603 "
            pdb=" O   GLY A 606 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OD2 ASP A 425 "
            pdb=" OG1 THR A 473 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ARG C 336 "
            pdb=" OG1 THR C 339 "
     model   vdw
     2.260 3.040
  ... (remaining 130239 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.080
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
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      :  0.010   0.110  16884  Z= 0.436
  Angle     :  1.257  17.540  22884  Z= 0.676
  Chirality :  0.067   0.400   2604
  Planarity :  0.009   0.077   2972
  Dihedral  : 11.165  75.772   6484
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.31 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.61 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.34 %
    Twisted General : 0.45 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.61 (0.15), residues: 2120
  helix: -2.79 (0.13), residues: 855
  sheet: -2.52 (0.30), residues: 229
  loop : -3.45 (0.16), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG D 374 
 TYR   0.039   0.004   TYR D 289 
 PHE   0.025   0.004   PHE A 467 
 TRP   0.037   0.005   TRP D 563 
 HIS   0.020   0.003   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.01007 (16884)
  covalent geometry    : angle       1.25710 (22884)
  hydrogen bonds       : bond        0.15022 (  630)
  hydrogen bonds       : angle       7.67376 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 405
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6708 (mtt) cc_final: 0.6262 (mtt)
REVERT: A  353 LEU cc_start: 0.7996 (mt) cc_final: 0.7774 (mt)
REVERT: A  366 ARG cc_start: 0.8425 (mpt-90) cc_final: 0.8173 (mtt90)
REVERT: A  425 ASP cc_start: 0.8147 (p0) cc_final: 0.7334 (p0)
REVERT: A  745 GLU cc_start: 0.8168 (mt-10) cc_final: 0.6994 (tm-30)
REVERT: B  378 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7458 (mtm180)
REVERT: B  380 SER cc_start: 0.8767 (t) cc_final: 0.8550 (t)
REVERT: B  387 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7650 (pp20)
REVERT: B  422 ASP cc_start: 0.8193 (m-30) cc_final: 0.7572 (m-30)
REVERT: B  484 ARG cc_start: 0.6506 (mmt180) cc_final: 0.6303 (mtp85)
REVERT: B  698 MET cc_start: 0.7082 (mmt) cc_final: 0.6754 (tpp)
REVERT: B  733 ILE cc_start: 0.8943 (mp) cc_final: 0.8731 (mm)
REVERT: B  748 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7713 (ptmm)
REVERT: C  258 MET cc_start: 0.3766 (mmt) cc_final: 0.2426 (mmt)
REVERT: C  405 LEU cc_start: 0.8972 (mt) cc_final: 0.8745 (mm)
REVERT: D  276 MET cc_start: 0.5103 (mmt) cc_final: 0.4815 (ptt)
REVERT: D  328 ARG cc_start: 0.8262 (mpt180) cc_final: 0.7929 (mmt-90)
REVERT: D  331 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7720 (mt-10)
REVERT: D  385 ARG cc_start: 0.7032 (ppt-90) cc_final: 0.6223 (mmt-90)
REVERT: D  439 MET cc_start: 0.8006 (tpt) cc_final: 0.7725 (tmm)
REVERT: D  659 ASN cc_start: 0.8421 (m-40) cc_final: 0.7805 (p0)
REVERT: D  698 MET cc_start: 0.5322 (mmm) cc_final: 0.4715 (mmm)
REVERT: D  705 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6220 (mt-10)
REVERT: D  719 LYS cc_start: 0.6900 (tttt) cc_final: 0.6482 (ttpt)
  outliers start: 6
  outliers final: 3
  residues processed: 410
  average time/residue: 0.1836
  time to fit residues: 103.4300
Evaluate side-chains
  239 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 236
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 200 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 449 ASN
A 472 ASN
A 475 GLN
A 495 ASN
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 598 GLN
B 319 HIS
B 377 HIS
B 449 ASN
B 475 GLN
B 510 GLN
B 726 HIS
C 277 GLN
C 472 ASN
C 499 GLN
C 726 HIS
D 377 HIS
D 411 GLN
D 593 GLN
D 628 GLN
D 726 HIS

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.134852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.107253 restraints weight = 51111.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.109217 restraints weight = 34288.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.111282 restraints weight = 22900.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.111366 restraints weight = 18853.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.111566 restraints weight = 16676.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7104
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16884  Z= 0.151
  Angle     :  0.785  13.164  22884  Z= 0.397
  Chirality :  0.048   0.324   2604
  Planarity :  0.006   0.056   2972
  Dihedral  :  7.027  46.717   2329
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.23 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.24 (0.16), residues: 2120
  helix: -1.28 (0.16), residues: 860
  sheet: -1.99 (0.30), residues: 222
  loop : -3.01 (0.17), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 519 
 TYR   0.020   0.002   TYR B 768 
 PHE   0.017   0.002   PHE A 466 
 TRP   0.031   0.002   TRP A 563 
 HIS   0.004   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (16884)
  covalent geometry    : angle       0.78505 (22884)
  hydrogen bonds       : bond        0.04220 (  630)
  hydrogen bonds       : angle       5.57372 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 302
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6122 (mtt) cc_final: 0.5817 (mtt)
REVERT: A  407 HIS cc_start: 0.8792 (m-70) cc_final: 0.8040 (m-70)
REVERT: A  422 ASP cc_start: 0.7626 (m-30) cc_final: 0.4196 (m-30)
REVERT: A  702 MET cc_start: 0.6893 (ptt) cc_final: 0.6135 (ptt)
REVERT: A  703 THR cc_start: 0.5999 (t) cc_final: 0.5708 (m)
REVERT: B  673 PRO cc_start: 0.7604 (Cg_exo) cc_final: 0.7358 (Cg_endo)
REVERT: B  733 ILE cc_start: 0.8920 (mp) cc_final: 0.8478 (mm)
REVERT: C  258 MET cc_start: 0.4265 (mmt) cc_final: 0.3018 (mmt)
REVERT: C  401 MET cc_start: 0.7726 (tpp) cc_final: 0.6647 (pmm)
REVERT: C  409 MET cc_start: 0.5784 (mmm) cc_final: 0.5480 (mmm)
REVERT: C  425 ASP cc_start: 0.7667 (p0) cc_final: 0.6895 (p0)
REVERT: C  553 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7895 (tttm)
REVERT: C  683 MET cc_start: 0.7686 (mtm) cc_final: 0.6301 (mtm)
REVERT: C  726 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7511 (t70)
REVERT: D  258 MET cc_start: 0.1951 (mtt) cc_final: 0.1333 (mtt)
REVERT: D  328 ARG cc_start: 0.8091 (mpt180) cc_final: 0.7852 (mmt-90)
REVERT: D  331 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7548 (mt-10)
REVERT: D  385 ARG cc_start: 0.7148 (ppt-90) cc_final: 0.6285 (mmt-90)
REVERT: D  557 PHE cc_start: 0.8512 (m-80) cc_final: 0.8070 (m-80)
REVERT: D  698 MET cc_start: 0.5357 (mmm) cc_final: 0.4629 (mmm)
REVERT: D  705 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6192 (mt-10)
  outliers start: 38
  outliers final: 21
  residues processed: 325
  average time/residue: 0.1593
  time to fit residues: 74.2297
Evaluate side-chains
  236 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  572 SER
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  699 ASP
Chi-restraints excluded: chain C residue  726 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  520 ILE
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 185 optimal weight:    9.9990
   chunk 159 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 183 optimal weight:    1.9990
   chunk 112 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 140 optimal weight:    0.3980
   chunk 34 optimal weight:    9.9990
   chunk 154 optimal weight:    0.9990
   chunk 153 optimal weight:    0.7980
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 510 GLN
B 726 HIS
D 319 HIS
** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.134748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.108049 restraints weight = 52126.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.109518 restraints weight = 34800.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.110473 restraints weight = 24139.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.110795 restraints weight = 21937.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.111119 restraints weight = 19615.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.3538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16884  Z= 0.132
  Angle     :  0.716  10.602  22884  Z= 0.361
  Chirality :  0.046   0.190   2604
  Planarity :  0.005   0.057   2972
  Dihedral  :  6.413  44.033   2327
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.00 %
    Favored  : 83.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.18), residues: 2120
  helix: -0.55 (0.18), residues: 856
  sheet: -1.81 (0.30), residues: 252
  loop : -2.71 (0.19), residues: 1012

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 503 
 TYR   0.014   0.001   TYR D 289 
 PHE   0.019   0.001   PHE D 467 
 TRP   0.017   0.001   TRP C 298 
 HIS   0.005   0.001   HIS C 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (16884)
  covalent geometry    : angle       0.71636 (22884)
  hydrogen bonds       : bond        0.03809 (  630)
  hydrogen bonds       : angle       5.23233 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 244
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.5817 (mtt) cc_final: 0.5610 (mtt)
REVERT: A  379 ILE cc_start: 0.8884 (tp) cc_final: 0.8537 (tp)
REVERT: A  401 MET cc_start: 0.7428 (tmm) cc_final: 0.7223 (tmm)
REVERT: A  407 HIS cc_start: 0.8829 (m-70) cc_final: 0.8357 (m-70)
REVERT: A  427 MET cc_start: 0.2585 (OUTLIER) cc_final: 0.2152 (mpp)
REVERT: A  657 PHE cc_start: 0.6950 (p90) cc_final: 0.6709 (p90)
REVERT: A  702 MET cc_start: 0.6886 (ptt) cc_final: 0.6256 (ptt)
REVERT: A  703 THR cc_start: 0.5895 (t) cc_final: 0.5655 (m)
REVERT: B  422 ASP cc_start: 0.7727 (m-30) cc_final: 0.7273 (m-30)
REVERT: B  673 PRO cc_start: 0.7671 (Cg_exo) cc_final: 0.7420 (Cg_endo)
REVERT: B  733 ILE cc_start: 0.8907 (mp) cc_final: 0.8651 (mm)
REVERT: C  258 MET cc_start: 0.4161 (mmt) cc_final: 0.2945 (mmt)
REVERT: C  401 MET cc_start: 0.6875 (tpp) cc_final: 0.6460 (pmm)
REVERT: C  409 MET cc_start: 0.5551 (mmm) cc_final: 0.5227 (mmm)
REVERT: C  425 ASP cc_start: 0.7574 (p0) cc_final: 0.6842 (p0)
REVERT: D  368 ILE cc_start: 0.9408 (mt) cc_final: 0.9053 (pt)
REVERT: D  385 ARG cc_start: 0.7071 (ppt-90) cc_final: 0.6281 (mmt-90)
REVERT: D  557 PHE cc_start: 0.8457 (m-80) cc_final: 0.8000 (m-80)
REVERT: D  598 GLN cc_start: 0.6128 (tp-100) cc_final: 0.5744 (mp10)
REVERT: D  698 MET cc_start: 0.5390 (mmm) cc_final: 0.5181 (tpt)
REVERT: D  705 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6032 (pt0)
REVERT: D  713 MET cc_start: 0.7947 (mmm) cc_final: 0.7035 (mmm)
REVERT: D  719 LYS cc_start: 0.6808 (ttpt) cc_final: 0.6545 (tttt)
  outliers start: 41
  outliers final: 24
  residues processed: 269
  average time/residue: 0.1478
  time to fit residues: 58.4882
Evaluate side-chains
  231 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 206
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 204 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 170 optimal weight:    7.9990
   chunk 186 optimal weight:    8.9990
   chunk 169 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 147 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 198 optimal weight:    5.9990
   chunk 115 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 726 HIS
D 346 ASN
D 727 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.132088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.105698 restraints weight = 52160.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.106032 restraints weight = 32261.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.107396 restraints weight = 26195.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.107721 restraints weight = 20042.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.108194 restraints weight = 18490.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  16884  Z= 0.193
  Angle     :  0.764  10.461  22884  Z= 0.385
  Chirality :  0.047   0.203   2604
  Planarity :  0.006   0.059   2972
  Dihedral  :  6.416  46.447   2327
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 14.79 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.18), residues: 2120
  helix: -0.38 (0.18), residues: 854
  sheet: -1.61 (0.31), residues: 251
  loop : -2.70 (0.19), residues: 1015

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 391 
 TYR   0.033   0.002   TYR C 768 
 PHE   0.021   0.002   PHE D 466 
 TRP   0.016   0.002   TRP D 563 
 HIS   0.007   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (16884)
  covalent geometry    : angle       0.76409 (22884)
  hydrogen bonds       : bond        0.04088 (  630)
  hydrogen bonds       : angle       5.34927 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 225
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6205 (mtt) cc_final: 0.5970 (mtt)
REVERT: A  366 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8000 (mpt90)
REVERT: A  401 MET cc_start: 0.7666 (tmm) cc_final: 0.7364 (tmm)
REVERT: A  513 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7431 (pt0)
REVERT: A  702 MET cc_start: 0.6976 (ptt) cc_final: 0.6099 (ptt)
REVERT: A  703 THR cc_start: 0.6159 (t) cc_final: 0.5847 (m)
REVERT: B  401 MET cc_start: 0.6056 (mmp) cc_final: 0.5354 (mmm)
REVERT: B  460 TYR cc_start: 0.5687 (t80) cc_final: 0.5485 (t80)
REVERT: B  504 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7223 (mp10)
REVERT: B  673 PRO cc_start: 0.7587 (Cg_exo) cc_final: 0.7369 (Cg_endo)
REVERT: B  691 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8771 (tt)
REVERT: C  258 MET cc_start: 0.4284 (mmt) cc_final: 0.3003 (mmt)
REVERT: C  401 MET cc_start: 0.6682 (tpp) cc_final: 0.6368 (pmm)
REVERT: C  409 MET cc_start: 0.5809 (mmm) cc_final: 0.5468 (mmm)
REVERT: C  425 ASP cc_start: 0.7489 (p0) cc_final: 0.6835 (p0)
REVERT: D  427 MET cc_start: 0.7858 (ptm) cc_final: 0.7514 (ptm)
REVERT: D  553 LYS cc_start: 0.6206 (pttt) cc_final: 0.5690 (pttm)
REVERT: D  557 PHE cc_start: 0.8579 (m-80) cc_final: 0.8238 (m-80)
REVERT: D  598 GLN cc_start: 0.6201 (tp-100) cc_final: 0.5798 (mp10)
REVERT: D  705 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6100 (pt0)
REVERT: D  713 MET cc_start: 0.7905 (mmm) cc_final: 0.7000 (mmm)
REVERT: D  719 LYS cc_start: 0.6805 (ttpt) cc_final: 0.6573 (tttt)
  outliers start: 62
  outliers final: 38
  residues processed: 263
  average time/residue: 0.1386
  time to fit residues: 53.7144
Evaluate side-chains
  242 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 201
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  596 THR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  342 LEU
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  531 ILE
Chi-restraints excluded: chain C residue  572 SER
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  632 VAL
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain C residue  726 HIS
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  378 ARG
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 152 optimal weight:    2.9990
   chunk 203 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 131 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 137 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 726 HIS
D 664 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.134198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.107528 restraints weight = 51703.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.108453 restraints weight = 33028.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.109670 restraints weight = 24806.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.110127 restraints weight = 21205.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.110219 restraints weight = 17818.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  16884  Z= 0.126
  Angle     :  0.688   8.986  22884  Z= 0.344
  Chirality :  0.045   0.204   2604
  Planarity :  0.005   0.059   2972
  Dihedral  :  5.996  48.358   2327
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.80 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.05 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.18), residues: 2120
  helix: -0.01 (0.18), residues: 856
  sheet: -1.30 (0.33), residues: 223
  loop : -2.46 (0.19), residues: 1041

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 582 
 TYR   0.014   0.001   TYR C 505 
 PHE   0.016   0.001   PHE D 466 
 TRP   0.016   0.001   TRP C 298 
 HIS   0.022   0.001   HIS C 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (16884)
  covalent geometry    : angle       0.68825 (22884)
  hydrogen bonds       : bond        0.03553 (  630)
  hydrogen bonds       : angle       4.90900 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 221
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6328 (mtt) cc_final: 0.5710 (mmt)
REVERT: A  366 ARG cc_start: 0.8347 (mtt90) cc_final: 0.8017 (mtt90)
REVERT: A  427 MET cc_start: 0.2665 (OUTLIER) cc_final: 0.2266 (mpp)
REVERT: A  431 TRP cc_start: 0.8046 (t-100) cc_final: 0.7651 (t60)
REVERT: A  485 MET cc_start: 0.8284 (mmm) cc_final: 0.7990 (mmt)
REVERT: A  702 MET cc_start: 0.6812 (ptt) cc_final: 0.5974 (ptt)
REVERT: A  703 THR cc_start: 0.5939 (t) cc_final: 0.5706 (m)
REVERT: B  401 MET cc_start: 0.5935 (mmp) cc_final: 0.5162 (mmm)
REVERT: B  504 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7222 (mp10)
REVERT: B  598 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7475 (tm-30)
REVERT: B  673 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7359 (Cg_endo)
REVERT: C  258 MET cc_start: 0.4395 (mmt) cc_final: 0.3146 (mmt)
REVERT: C  401 MET cc_start: 0.6721 (tpp) cc_final: 0.6485 (pmm)
REVERT: C  409 MET cc_start: 0.5663 (mmm) cc_final: 0.5352 (mmm)
REVERT: C  425 ASP cc_start: 0.7636 (p0) cc_final: 0.6993 (p0)
REVERT: D  385 ARG cc_start: 0.7427 (ppt-90) cc_final: 0.6570 (mmt90)
REVERT: D  427 MET cc_start: 0.7741 (ptm) cc_final: 0.7212 (ptm)
REVERT: D  553 LYS cc_start: 0.6127 (pttt) cc_final: 0.5337 (pttm)
REVERT: D  557 PHE cc_start: 0.8525 (m-80) cc_final: 0.8149 (m-80)
REVERT: D  705 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6061 (pt0)
REVERT: D  713 MET cc_start: 0.8011 (mmm) cc_final: 0.7126 (mmm)
  outliers start: 50
  outliers final: 30
  residues processed: 251
  average time/residue: 0.1355
  time to fit residues: 51.1880
Evaluate side-chains
  230 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 197
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain A residue  453 ASP
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  572 SER
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  378 ARG
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  702 MET
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 146 optimal weight:    2.9990
   chunk 127 optimal weight:    0.6980
   chunk 174 optimal weight:    0.9980
   chunk 55 optimal weight:    9.9990
   chunk 117 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0170
   chunk 203 optimal weight:    9.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 407 HIS
C 664 HIS
D 340 GLN
D 499 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.135437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.107632 restraints weight = 53101.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.109658 restraints weight = 37345.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.110681 restraints weight = 24464.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.111047 restraints weight = 22141.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.111265 restraints weight = 19690.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.4433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16884  Z= 0.115
  Angle     :  0.671  10.456  22884  Z= 0.332
  Chirality :  0.044   0.222   2604
  Planarity :  0.005   0.057   2972
  Dihedral  :  5.600  50.066   2327
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.31 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.18), residues: 2120
  helix:  0.35 (0.18), residues: 856
  sheet: -1.43 (0.36), residues: 188
  loop : -2.25 (0.19), residues: 1076

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 545 
 TYR   0.013   0.001   TYR C 505 
 PHE   0.018   0.001   PHE A 466 
 TRP   0.014   0.001   TRP C 298 
 HIS   0.010   0.001   HIS D 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (16884)
  covalent geometry    : angle       0.67125 (22884)
  hydrogen bonds       : bond        0.03305 (  630)
  hydrogen bonds       : angle       4.60860 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 241
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7237 (mm)
REVERT: A  372 MET cc_start: 0.7137 (tpp) cc_final: 0.6548 (ttm)
REVERT: A  427 MET cc_start: 0.2460 (OUTLIER) cc_final: 0.2050 (mpp)
REVERT: A  657 PHE cc_start: 0.6968 (p90) cc_final: 0.6756 (p90)
REVERT: A  702 MET cc_start: 0.6724 (ptt) cc_final: 0.6080 (ptp)
REVERT: A  703 THR cc_start: 0.6030 (t) cc_final: 0.5822 (m)
REVERT: B  401 MET cc_start: 0.5766 (mmp) cc_final: 0.5425 (mmm)
REVERT: B  422 ASP cc_start: 0.7984 (m-30) cc_final: 0.7083 (m-30)
REVERT: B  484 ARG cc_start: 0.5714 (mmt-90) cc_final: 0.5404 (mtp85)
REVERT: B  504 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7071 (mp10)
REVERT: B  566 LEU cc_start: 0.8001 (tp) cc_final: 0.7775 (tp)
REVERT: B  598 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7477 (tm-30)
REVERT: B  673 PRO cc_start: 0.7775 (Cg_exo) cc_final: 0.7551 (Cg_endo)
REVERT: B  756 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7668 (mm)
REVERT: C  258 MET cc_start: 0.4266 (mmt) cc_final: 0.2939 (mmt)
REVERT: C  405 LEU cc_start: 0.9032 (mm) cc_final: 0.8698 (mm)
REVERT: C  409 MET cc_start: 0.5582 (mmm) cc_final: 0.5375 (mmm)
REVERT: C  425 ASP cc_start: 0.7585 (p0) cc_final: 0.6984 (p0)
REVERT: D  385 ARG cc_start: 0.7327 (ppt-90) cc_final: 0.6473 (mmt90)
REVERT: D  427 MET cc_start: 0.7794 (ptm) cc_final: 0.7436 (ptm)
REVERT: D  553 LYS cc_start: 0.6413 (pttt) cc_final: 0.5685 (pttm)
REVERT: D  557 PHE cc_start: 0.8515 (m-80) cc_final: 0.8146 (m-80)
REVERT: D  657 PHE cc_start: 0.7395 (p90) cc_final: 0.7071 (p90)
REVERT: D  705 GLU cc_start: 0.6554 (mt-10) cc_final: 0.6045 (pt0)
REVERT: D  713 MET cc_start: 0.7975 (mmm) cc_final: 0.7111 (mmm)
  outliers start: 52
  outliers final: 35
  residues processed: 275
  average time/residue: 0.1321
  time to fit residues: 54.6849
Evaluate side-chains
  250 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 210
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain A residue  453 ASP
Chi-restraints excluded: chain A residue  545 ARG
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  756 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  572 SER
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  642 THR
Chi-restraints excluded: chain C residue  664 HIS
Chi-restraints excluded: chain C residue  665 VAL
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  354 VAL
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  663 LEU
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 176 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 200 optimal weight:    4.9990
   chunk 131 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    7.9990
   chunk 185 optimal weight:    8.9990
   chunk 47 optimal weight:    7.9990
   chunk 147 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 188 optimal weight:    0.0370
   overall best weight:    3.0066

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

Flipped N/Q/H residues before XYZ refinement:
A 510 GLN
C 278 GLN
C 499 GLN
C 726 HIS
D 499 GLN
D 593 GLN
** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.132111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.105139 restraints weight = 52842.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.106067 restraints weight = 34060.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.107277 restraints weight = 25068.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.107245 restraints weight = 22350.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.107570 restraints weight = 20328.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  16884  Z= 0.205
  Angle     :  0.767  14.013  22884  Z= 0.379
  Chirality :  0.046   0.238   2604
  Planarity :  0.006   0.060   2972
  Dihedral  :  5.830  51.145   2327
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.93 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.18), residues: 2120
  helix:  0.12 (0.18), residues: 864
  sheet: -1.35 (0.32), residues: 260
  loop : -2.34 (0.20), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 378 
 TYR   0.019   0.002   TYR D 643 
 PHE   0.012   0.002   PHE B 451 
 TRP   0.017   0.002   TRP D 563 
 HIS   0.018   0.001   HIS C 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (16884)
  covalent geometry    : angle       0.76687 (22884)
  hydrogen bonds       : bond        0.03841 (  630)
  hydrogen bonds       : angle       4.98735 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 214
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7306 (mm)
REVERT: A  366 ARG cc_start: 0.8205 (mtt90) cc_final: 0.7907 (mtt90)
REVERT: A  372 MET cc_start: 0.7309 (tpp) cc_final: 0.6497 (ttm)
REVERT: A  401 MET cc_start: 0.7569 (tpp) cc_final: 0.6144 (pmm)
REVERT: A  482 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8044 (mm)
REVERT: A  702 MET cc_start: 0.6825 (ptt) cc_final: 0.6046 (ptt)
REVERT: A  703 THR cc_start: 0.6200 (t) cc_final: 0.5884 (m)
REVERT: B  401 MET cc_start: 0.5936 (mmp) cc_final: 0.5505 (mmm)
REVERT: B  484 ARG cc_start: 0.5975 (mmt-90) cc_final: 0.5577 (mmt180)
REVERT: B  504 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7206 (mp10)
REVERT: B  598 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7436 (tm-30)
REVERT: B  673 PRO cc_start: 0.7753 (Cg_exo) cc_final: 0.7549 (Cg_endo)
REVERT: B  756 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7716 (mm)
REVERT: C  258 MET cc_start: 0.4289 (mmt) cc_final: 0.3057 (mmt)
REVERT: C  405 LEU cc_start: 0.9051 (mm) cc_final: 0.8744 (mm)
REVERT: C  409 MET cc_start: 0.5759 (mmm) cc_final: 0.5525 (mmm)
REVERT: C  425 ASP cc_start: 0.7678 (p0) cc_final: 0.7092 (p0)
REVERT: D  385 ARG cc_start: 0.7352 (ppt-90) cc_final: 0.6492 (mmt90)
REVERT: D  553 LYS cc_start: 0.6246 (pttt) cc_final: 0.5896 (pttt)
REVERT: D  557 PHE cc_start: 0.8561 (m-80) cc_final: 0.8208 (m-80)
REVERT: D  705 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6150 (pt0)
REVERT: D  713 MET cc_start: 0.8108 (mmm) cc_final: 0.7314 (mmm)
  outliers start: 61
  outliers final: 45
  residues processed: 257
  average time/residue: 0.1339
  time to fit residues: 52.5928
Evaluate side-chains
  254 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 204
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  756 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  476 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  574 ILE
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  632 VAL
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain C residue  726 HIS
Chi-restraints excluded: chain C residue  759 VAL
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  476 THR
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 161 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 203 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 128 optimal weight:    3.9990
   chunk 205 optimal weight:    0.2980
   chunk 145 optimal weight:    1.9990
   chunk 157 optimal weight:    5.9990
   chunk 171 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.8588

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
A 510 GLN
** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.131744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.105545 restraints weight = 53041.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.106891 restraints weight = 35937.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.107728 restraints weight = 24306.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.107898 restraints weight = 21457.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.108052 restraints weight = 20485.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.4514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  16884  Z= 0.193
  Angle     :  0.783  14.496  22884  Z= 0.384
  Chirality :  0.047   0.244   2604
  Planarity :  0.005   0.059   2972
  Dihedral  :  5.960  52.143   2327
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.99 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.18), residues: 2120
  helix:  0.13 (0.18), residues: 858
  sheet: -1.17 (0.33), residues: 248
  loop : -2.36 (0.20), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 378 
 TYR   0.025   0.002   TYR D 643 
 PHE   0.019   0.002   PHE D 466 
 TRP   0.018   0.002   TRP D 563 
 HIS   0.019   0.001   HIS C 726 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (16884)
  covalent geometry    : angle       0.78251 (22884)
  hydrogen bonds       : bond        0.03892 (  630)
  hydrogen bonds       : angle       5.04479 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 210
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7385 (mm)
REVERT: A  366 ARG cc_start: 0.8206 (mtt90) cc_final: 0.7931 (mtt90)
REVERT: A  372 MET cc_start: 0.7199 (tpp) cc_final: 0.6271 (ttm)
REVERT: A  401 MET cc_start: 0.7364 (tpp) cc_final: 0.6182 (pmm)
REVERT: A  485 MET cc_start: 0.7951 (mmm) cc_final: 0.7737 (mmm)
REVERT: A  702 MET cc_start: 0.6908 (ptt) cc_final: 0.6109 (ptt)
REVERT: A  703 THR cc_start: 0.6214 (t) cc_final: 0.5982 (m)
REVERT: B  401 MET cc_start: 0.5727 (mmp) cc_final: 0.5410 (mmm)
REVERT: B  484 ARG cc_start: 0.5921 (mmt-90) cc_final: 0.5615 (mmt180)
REVERT: B  504 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7261 (mp10)
REVERT: B  598 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7312 (tm-30)
REVERT: B  673 PRO cc_start: 0.7797 (Cg_exo) cc_final: 0.7592 (Cg_endo)
REVERT: B  756 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7733 (mt)
REVERT: C  258 MET cc_start: 0.4042 (mmt) cc_final: 0.2840 (mmt)
REVERT: C  405 LEU cc_start: 0.9107 (mm) cc_final: 0.8829 (mm)
REVERT: C  425 ASP cc_start: 0.7618 (p0) cc_final: 0.7119 (p0)
REVERT: D  276 MET cc_start: 0.6123 (tmm) cc_final: 0.5865 (tmm)
REVERT: D  553 LYS cc_start: 0.6124 (pttt) cc_final: 0.5857 (pttt)
REVERT: D  557 PHE cc_start: 0.8468 (m-80) cc_final: 0.8182 (m-80)
REVERT: D  643 TYR cc_start: 0.8205 (t80) cc_final: 0.7713 (t80)
REVERT: D  705 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6163 (pt0)
REVERT: D  713 MET cc_start: 0.8158 (mmm) cc_final: 0.7375 (mmm)
  outliers start: 65
  outliers final: 52
  residues processed: 258
  average time/residue: 0.1330
  time to fit residues: 52.3019
Evaluate side-chains
  256 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 200
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  427 MET
Chi-restraints excluded: chain A residue  453 ASP
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  762 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  453 ASP
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  702 MET
Chi-restraints excluded: chain B residue  756 ILE
Chi-restraints excluded: chain B residue  771 LEU
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  476 THR
Chi-restraints excluded: chain C residue  494 THR
Chi-restraints excluded: chain C residue  505 TYR
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  574 ILE
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  632 VAL
Chi-restraints excluded: chain C residue  642 THR
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain C residue  759 VAL
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  476 THR
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  687 ILE
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 3 optimal weight:   20.0000
   chunk 118 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 200 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 151 optimal weight:    0.0170
   chunk 188 optimal weight:    0.0370
   overall best weight:    0.7698

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

Flipped N/Q/H residues before XYZ refinement:
C 664 HIS
C 726 HIS
D 499 GLN
D 664 HIS
D 727 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.134664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.107700 restraints weight = 52120.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.108998 restraints weight = 32603.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.110006 restraints weight = 23062.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.110147 restraints weight = 21699.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.110189 restraints weight = 18954.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16884  Z= 0.122
  Angle     :  0.726  13.235  22884  Z= 0.354
  Chirality :  0.045   0.254   2604
  Planarity :  0.005   0.056   2972
  Dihedral  :  5.605  53.075   2327
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.34 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.19), residues: 2120
  helix:  0.46 (0.18), residues: 860
  sheet: -1.32 (0.33), residues: 233
  loop : -2.20 (0.20), residues: 1027

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 582 
 TYR   0.017   0.001   TYR D 643 
 PHE   0.013   0.001   PHE D 466 
 TRP   0.018   0.001   TRP B 298 
 HIS   0.004   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (16884)
  covalent geometry    : angle       0.72595 (22884)
  hydrogen bonds       : bond        0.03412 (  630)
  hydrogen bonds       : angle       4.67787 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 219
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7177 (mm)
REVERT: A  366 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7848 (mtt90)
REVERT: A  372 MET cc_start: 0.7339 (tpp) cc_final: 0.6411 (ttm)
REVERT: A  401 MET cc_start: 0.7667 (tpp) cc_final: 0.6424 (pmm)
REVERT: A  420 LEU cc_start: 0.8557 (tt) cc_final: 0.8356 (tp)
REVERT: A  702 MET cc_start: 0.6743 (ptt) cc_final: 0.5966 (ptt)
REVERT: A  703 THR cc_start: 0.6058 (t) cc_final: 0.5846 (m)
REVERT: B  401 MET cc_start: 0.5807 (mmp) cc_final: 0.5482 (mmm)
REVERT: B  504 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7161 (mp10)
REVERT: B  598 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7394 (tm-30)
REVERT: B  673 PRO cc_start: 0.7754 (Cg_exo) cc_final: 0.7527 (Cg_endo)
REVERT: B  756 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7682 (mm)
REVERT: C  258 MET cc_start: 0.4450 (mmt) cc_final: 0.3168 (mmt)
REVERT: C  425 ASP cc_start: 0.7600 (p0) cc_final: 0.7105 (p0)
REVERT: D  385 ARG cc_start: 0.7327 (ppt-90) cc_final: 0.6510 (mmt90)
REVERT: D  553 LYS cc_start: 0.6534 (pttt) cc_final: 0.5792 (pttm)
REVERT: D  557 PHE cc_start: 0.8587 (m-80) cc_final: 0.8239 (m-80)
REVERT: D  657 PHE cc_start: 0.7214 (p90) cc_final: 0.6978 (p90)
REVERT: D  698 MET cc_start: 0.3620 (tpt) cc_final: 0.3302 (tpp)
REVERT: D  705 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6105 (pt0)
REVERT: D  713 MET cc_start: 0.8115 (mmm) cc_final: 0.7282 (mmm)
REVERT: D  740 GLU cc_start: 0.8877 (pt0) cc_final: 0.8650 (pp20)
  outliers start: 48
  outliers final: 36
  residues processed: 254
  average time/residue: 0.1268
  time to fit residues: 49.2232
Evaluate side-chains
  244 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 ASP
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  756 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  379 ILE
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  664 HIS
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain C residue  726 HIS
Chi-restraints excluded: chain D residue  262 VAL
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 142 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0970
   chunk 27 optimal weight:    8.9990
   chunk 174 optimal weight:    9.9990
   chunk 167 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 664 HIS
C 726 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.134692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.108307 restraints weight = 53326.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.109482 restraints weight = 36035.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.109784 restraints weight = 25514.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.110218 restraints weight = 25117.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.111565 restraints weight = 21418.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16884  Z= 0.126
  Angle     :  0.735  12.681  22884  Z= 0.358
  Chirality :  0.045   0.260   2604
  Planarity :  0.005   0.056   2972
  Dihedral  :  5.472  53.566   2327
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.07 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.19), residues: 2120
  helix:  0.46 (0.18), residues: 853
  sheet: -1.29 (0.33), residues: 234
  loop : -2.11 (0.20), residues: 1033

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 503 
 TYR   0.015   0.001   TYR D 643 
 PHE   0.015   0.001   PHE D 466 
 TRP   0.027   0.001   TRP B 298 
 HIS   0.008   0.001   HIS C 664 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (16884)
  covalent geometry    : angle       0.73530 (22884)
  hydrogen bonds       : bond        0.03383 (  630)
  hydrogen bonds       : angle       4.63373 ( 1818)

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

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

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4240 Ramachandran restraints generated.
    2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 213
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7160 (mm)
REVERT: A  372 MET cc_start: 0.7179 (tpp) cc_final: 0.6318 (ttm)
REVERT: A  401 MET cc_start: 0.7582 (tpp) cc_final: 0.6413 (pmm)
REVERT: A  420 LEU cc_start: 0.8568 (tt) cc_final: 0.8351 (tp)
REVERT: A  702 MET cc_start: 0.6763 (ptt) cc_final: 0.6015 (ptt)
REVERT: A  713 MET cc_start: 0.8758 (mmm) cc_final: 0.8437 (mpp)
REVERT: B  401 MET cc_start: 0.5602 (mmp) cc_final: 0.5266 (mmm)
REVERT: B  504 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7084 (mp10)
REVERT: B  598 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7012 (tm-30)
REVERT: B  673 PRO cc_start: 0.7847 (Cg_exo) cc_final: 0.7638 (Cg_endo)
REVERT: B  756 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7661 (mm)
REVERT: C  258 MET cc_start: 0.4325 (mmt) cc_final: 0.3097 (mmt)
REVERT: C  291 ASP cc_start: 0.8846 (m-30) cc_final: 0.8446 (m-30)
REVERT: C  425 ASP cc_start: 0.7571 (p0) cc_final: 0.7082 (p0)
REVERT: D  385 ARG cc_start: 0.7219 (ppt-90) cc_final: 0.6432 (mmt90)
REVERT: D  553 LYS cc_start: 0.6473 (pttt) cc_final: 0.5685 (pttm)
REVERT: D  557 PHE cc_start: 0.8586 (m-80) cc_final: 0.8262 (m-80)
REVERT: D  657 PHE cc_start: 0.7133 (p90) cc_final: 0.6911 (p90)
REVERT: D  698 MET cc_start: 0.3691 (tpt) cc_final: 0.3378 (tpp)
REVERT: D  705 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6126 (pt0)
REVERT: D  713 MET cc_start: 0.8116 (mmm) cc_final: 0.7314 (mmm)
REVERT: D  740 GLU cc_start: 0.8847 (pt0) cc_final: 0.8611 (pp20)
  outliers start: 42
  outliers final: 36
  residues processed: 244
  average time/residue: 0.1259
  time to fit residues: 48.0279
Evaluate side-chains
  244 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 HIS
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  389 GLU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 ASP
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  769 LEU
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  393 HIS
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  580 ILE
Chi-restraints excluded: chain B residue  590 THR
Chi-restraints excluded: chain B residue  598 GLN
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue  624 SER
Chi-restraints excluded: chain B residue  658 TYR
Chi-restraints excluded: chain B residue  678 SER
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  756 ILE
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  379 ILE
Chi-restraints excluded: chain C residue  412 VAL
Chi-restraints excluded: chain C residue  414 VAL
Chi-restraints excluded: chain C residue  469 THR
Chi-restraints excluded: chain C residue  520 ILE
Chi-restraints excluded: chain C residue  574 ILE
Chi-restraints excluded: chain C residue  580 ILE
Chi-restraints excluded: chain C residue  632 VAL
Chi-restraints excluded: chain C residue  664 HIS
Chi-restraints excluded: chain C residue  681 ILE
Chi-restraints excluded: chain C residue  702 MET
Chi-restraints excluded: chain C residue  726 HIS
Chi-restraints excluded: chain D residue  353 LEU
Chi-restraints excluded: chain D residue  401 MET
Chi-restraints excluded: chain D residue  682 THR
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  765 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 212
   random chunks:
   chunk 185 optimal weight:    6.9990
   chunk 205 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 158 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 123 optimal weight:    7.9990
   chunk 195 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 203 optimal weight:    0.0670
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.4124

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

Flipped N/Q/H residues before XYZ refinement:
A 407 HIS
C 664 HIS
** C 726 HIS ** 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 = 0.4281 r_free = 0.4281 target = 0.134148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.106531 restraints weight = 51869.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.108067 restraints weight = 33659.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.109507 restraints weight = 23409.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.110081 restraints weight = 18675.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.110465 restraints weight = 16816.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  16884  Z= 0.137
  Angle     :  0.745  12.162  22884  Z= 0.363
  Chirality :  0.045   0.259   2604
  Planarity :  0.005   0.061   2972
  Dihedral  :  5.453  54.050   2327
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.13 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.19), residues: 2120
  helix:  0.46 (0.18), residues: 860
  sheet: -1.13 (0.34), residues: 218
  loop : -2.14 (0.20), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 503 
 TYR   0.016   0.001   TYR D 643 
 PHE   0.014   0.002   PHE B 451 
 TRP   0.019   0.001   TRP B 298 
 HIS   0.003   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (16884)
  covalent geometry    : angle       0.74477 (22884)
  hydrogen bonds       : bond        0.03417 (  630)
  hydrogen bonds       : angle       4.66725 ( 1818)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2966.53 seconds
wall clock time: 51 minutes 57.13 seconds (3117.13 seconds total)