Starting phenix.real_space_refine
on Wed Mar  4 04:54:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ijz_9682/03_2026/6ijz_9682.map"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.014
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      50      5.16       5
     C    7264      2.51       5
     N    1778      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  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: 10964
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5482
          Classifications: {'peptide': 683}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.63, per 1000 atoms: 0.42
  Number of scatterers: 10964
  At special positions: 0
  Unit cell: (95.411, 139.849, 108.481, 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      50     16.00
     O    1872      8.00
     N    1778      7.00
     C    7264      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 634.5 milliseconds
  

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 2 sheets defined
      69.2% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.804A  pdb=" N   VAL A   9 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 77 through 81
      removed outlier: 3.656A  pdb=" N   LYS A  81 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 93 through 125
      removed outlier: 3.744A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
      removed outlier: 3.891A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 121 " --> pdb=" O   TRP A 117 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 158 through 193
      removed outlier: 4.010A  pdb=" N   HIS A 162 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL A 164 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TRP A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   CYS A 174 " --> pdb=" O   THR A 170 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 185 " --> pdb=" O   TYR A 181 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET A 187 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 4.040A  pdb=" N   LEU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 267
      removed outlier: 3.546A  pdb=" N   GLN A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 267 " --> pdb=" O   GLN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 310
      removed outlier: 5.250A  pdb=" N   ALA A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 337
      removed outlier: 3.562A  pdb=" N   ALA A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.595A  pdb=" N   ARG A 374 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 382 " --> pdb=" O   MET A 378 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 3.508A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL A 396 " --> pdb=" O   PRO A 392 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 399 " --> pdb=" O   PHE A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 420 through 428
    Processing helix  chain 'A' and resid 428 through 438
    Processing helix  chain 'A' and resid 440 through 452
      removed outlier: 3.961A  pdb=" N   GLU A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 475
      removed outlier: 4.215A  pdb=" N   ARG A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 489
      removed outlier: 3.822A  pdb=" N   ALA A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   PHE A 487 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 496
      removed outlier: 3.609A  pdb=" N   GLN A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 3.739A  pdb=" N   ILE A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE A 509 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 513 through 523
    Processing helix  chain 'A' and resid 524 through 530
    Processing helix  chain 'A' and resid 534 through 547
      removed outlier: 4.112A  pdb=" N   MET A 540 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
      removed outlier: 3.514A  pdb=" N   ALA A 558 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET A 559 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 583
      removed outlier: 3.848A  pdb=" N   ILE A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 574 " --> pdb=" O   GLU A 570 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 583 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.948A  pdb=" N   ILE A 603 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 647
      removed outlier: 3.773A  pdb=" N   GLY A 629 " --> pdb=" O   PRO A 625 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 644 " --> pdb=" O   LEU A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.838A  pdb=" N   ALA A 654 " --> pdb=" O   ALA A 651 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A 655 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 651 through 655'
    Processing helix  chain 'A' and resid 659 through 676
      removed outlier: 3.852A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 666 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 680
    Processing helix  chain 'A' and resid 684 through 699
      removed outlier: 3.636A  pdb=" N   ASP A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 709
      removed outlier: 3.582A  pdb=" N   GLN A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 30
      removed outlier: 3.804A  pdb=" N   VAL B   9 " --> pdb=" O   GLN B   5 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 39 through 45
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.656A  pdb=" N   LYS B  81 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 93 through 125
      removed outlier: 3.744A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      removed outlier: 3.891A  pdb=" N   VAL B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 121 " --> pdb=" O   TRP B 117 " (cutoff:3.500A)
      Proline residue:  B 122  - end of helix
    Processing helix  chain 'B' and resid 158 through 193
      removed outlier: 4.009A  pdb=" N   HIS B 162 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL B 164 " --> pdb=" O   TRP B 160 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TRP B 172 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   CYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B 185 " --> pdb=" O   TYR B 181 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET B 187 " --> pdb=" O   THR B 183 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 4.040A  pdb=" N   LEU B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 267
      removed outlier: 3.546A  pdb=" N   GLN B 263 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR B 266 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA B 267 " --> pdb=" O   GLN B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 310
      removed outlier: 5.250A  pdb=" N   ALA B 296 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER B 306 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 337
      removed outlier: 3.561A  pdb=" N   ALA B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
      removed outlier: 3.596A  pdb=" N   ARG B 374 " --> pdb=" O   SER B 370 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE B 382 " --> pdb=" O   MET B 378 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 387 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 401
      removed outlier: 3.508A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 396 " --> pdb=" O   PRO B 392 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU B 399 " --> pdb=" O   PHE B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 407
    Processing helix  chain 'B' and resid 420 through 428
    Processing helix  chain 'B' and resid 428 through 438
    Processing helix  chain 'B' and resid 440 through 452
      removed outlier: 3.961A  pdb=" N   GLU B 452 " --> pdb=" O   MET B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 475
      removed outlier: 4.215A  pdb=" N   ARG B 462 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 489
      removed outlier: 3.822A  pdb=" N   ALA B 483 " --> pdb=" O   ALA B 479 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 486 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   PHE B 487 " --> pdb=" O   ALA B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 496
      removed outlier: 3.608A  pdb=" N   GLN B 496 " --> pdb=" O   SER B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 512
      removed outlier: 3.739A  pdb=" N   ILE B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE B 509 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 513 through 523
    Processing helix  chain 'B' and resid 524 through 530
    Processing helix  chain 'B' and resid 534 through 547
      removed outlier: 4.112A  pdb=" N   MET B 540 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
      removed outlier: 3.514A  pdb=" N   ALA B 558 " --> pdb=" O   ARG B 555 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET B 559 " --> pdb=" O   GLU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 583
      removed outlier: 3.848A  pdb=" N   ILE B 573 " --> pdb=" O   GLY B 569 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN B 574 " --> pdb=" O   GLU B 570 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TYR B 583 " --> pdb=" O   LEU B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.947A  pdb=" N   ILE B 603 " --> pdb=" O   ALA B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 647
      removed outlier: 3.773A  pdb=" N   GLY B 629 " --> pdb=" O   PRO B 625 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY B 644 " --> pdb=" O   LEU B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 655
      removed outlier: 3.837A  pdb=" N   ALA B 654 " --> pdb=" O   ALA B 651 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B 655 " --> pdb=" O   ALA B 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 651 through 655'
    Processing helix  chain 'B' and resid 659 through 676
      removed outlier: 3.852A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 666 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 674 " --> pdb=" O   HIS B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 680
    Processing helix  chain 'B' and resid 684 through 699
      removed outlier: 3.636A  pdb=" N   ASP B 692 " --> pdb=" O   ALA B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 709
      removed outlier: 3.581A  pdb=" N   GLN B 709 " --> pdb=" O   LYS B 705 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205
      removed outlier: 4.859A  pdb=" N   VAL A 239 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205
      removed outlier: 4.860A  pdb=" N   VAL B 239 " --> pdb=" O   MET B 320 " (cutoff:3.500A)

    557 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3027
        1.33 -     1.45: 2070
        1.45 -     1.57: 6083
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 11272
  Sorted by residual:
  bond pdb=" CB  TRP A 624 "
       pdb=" CG  TRP A 624 "
    ideal  model  delta    sigma   weight residual
    1.498  1.404  0.094 3.10e-02 1.04e+03 9.10e+00
  bond pdb=" CB  TRP B 624 "
       pdb=" CG  TRP B 624 "
    ideal  model  delta    sigma   weight residual
    1.498  1.405  0.093 3.10e-02 1.04e+03 9.04e+00
  bond pdb=" CB  PRO B 111 "
       pdb=" CG  PRO B 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.54e+00
  bond pdb=" CB  PRO A 111 "
       pdb=" CG  PRO A 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.54e+00
  bond pdb=" CB  TRP B 172 "
       pdb=" CG  TRP B 172 "
    ideal  model  delta    sigma   weight residual
    1.498  1.443  0.055 3.10e-02 1.04e+03 3.15e+00
  ... (remaining 11267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 14665
        2.32 -     4.64: 541
        4.64 -     6.97: 96
        6.97 -     9.29: 40
        9.29 -    11.61: 6
  Bond angle restraints: 15348
  Sorted by residual:
  angle pdb=" C   SER B 619 "
        pdb=" N   ALA B 620 "
        pdb=" CA  ALA B 620 "
      ideal   model   delta    sigma   weight residual
     121.70  133.31  -11.61 1.80e+00 3.09e-01 4.16e+01
  angle pdb=" C   SER A 619 "
        pdb=" N   ALA A 620 "
        pdb=" CA  ALA A 620 "
      ideal   model   delta    sigma   weight residual
     121.70  133.31  -11.61 1.80e+00 3.09e-01 4.16e+01
  angle pdb=" C   VAL A 206 "
        pdb=" N   ARG A 207 "
        pdb=" CA  ARG A 207 "
      ideal   model   delta    sigma   weight residual
     121.54  130.94   -9.40 1.91e+00 2.74e-01 2.42e+01
  angle pdb=" C   VAL B 206 "
        pdb=" N   ARG B 207 "
        pdb=" CA  ARG B 207 "
      ideal   model   delta    sigma   weight residual
     121.54  130.89   -9.35 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" CA  TRP B 624 "
        pdb=" CB  TRP B 624 "
        pdb=" CG  TRP B 624 "
      ideal   model   delta    sigma   weight residual
     113.60  104.68    8.92 1.90e+00 2.77e-01 2.20e+01
  ... (remaining 15343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.25: 5910
       12.25 -    24.50: 580
       24.50 -    36.75: 120
       36.75 -    49.00: 32
       49.00 -    61.25: 4
  Dihedral angle restraints: 6646
    sinusoidal: 2596
      harmonic: 4050
  Sorted by residual:
  dihedral pdb=" CA  GLN B 135 "
           pdb=" C   GLN B 135 "
           pdb=" N   LEU B 136 "
           pdb=" CA  LEU B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.79  -48.21     0      5.00e+00 4.00e-02 9.29e+01
  dihedral pdb=" CA  GLN A 135 "
           pdb=" C   GLN A 135 "
           pdb=" N   LEU A 136 "
           pdb=" CA  LEU A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.83  -48.17     0      5.00e+00 4.00e-02 9.28e+01
  dihedral pdb=" CA  LYS A 134 "
           pdb=" C   LYS A 134 "
           pdb=" N   GLN A 135 "
           pdb=" CA  GLN A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.87   31.13     0      5.00e+00 4.00e-02 3.88e+01
  ... (remaining 6643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1371
       0.073 -    0.146: 326
       0.146 -    0.218: 34
       0.218 -    0.291: 11
       0.291 -    0.364: 2
  Chirality restraints: 1744
  Sorted by residual:
  chirality pdb=" CB  VAL A 206 "
            pdb=" CA  VAL A 206 "
            pdb=" CG1 VAL A 206 "
            pdb=" CG2 VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CB  VAL B 206 "
            pdb=" CA  VAL B 206 "
            pdb=" CG1 VAL B 206 "
            pdb=" CG2 VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CA  TYR A 613 "
            pdb=" N   TYR A 613 "
            pdb=" C   TYR A 613 "
            pdb=" CB  TYR A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1741 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 233 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.03e+01
        pdb=" C   TYR B 233 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   TYR B 233 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 234 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 233 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   TYR A 233 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TYR A 233 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 234 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 612 "    0.014 2.00e-02 2.50e+03   3.01e-02 9.03e+00
        pdb=" C   VAL A 612 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   VAL A 612 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 613 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 52
        2.58 -     3.16: 8901
        3.16 -     3.74: 16886
        3.74 -     4.32: 22900
        4.32 -     4.90: 37417
  Nonbonded interactions: 86156
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 612 "
            pdb=" CD1 TYR B 613 "
     model   vdw
     2.000 3.340
  nonbonded pdb=" O   VAL A 612 "
            pdb=" CD1 TYR A 613 "
     model   vdw
     2.001 3.340
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OE1 GLU A 219 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OE1 GLU B 219 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   PHE B 420 "
            pdb=" OG  SER B 423 "
     model   vdw
     2.314 3.040
  ... (remaining 86151 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
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      :  0.008   0.094  11272  Z= 0.323
  Angle     :  1.110  11.610  15348  Z= 0.589
  Chirality :  0.064   0.364   1744
  Planarity :  0.009   0.068   1914
  Dihedral  : 10.644  61.249   4010
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.93 %
    Favored  : 88.77 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.45 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.78 %
    Twisted General : 0.31 %

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: -5.03 (0.17), residues: 1354
  helix: -2.86 (0.13), residues: 860
  sheet: -3.31 (1.09), residues: 20
  loop : -4.03 (0.23), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 630 
 TYR   0.048   0.003   TYR A 181 
 PHE   0.029   0.003   PHE A  21 
 TRP   0.043   0.004   TRP A 525 
 HIS   0.009   0.002   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00764 (11272)
  covalent geometry    : angle       1.10977 (15348)
  hydrogen bonds       : bond        0.15687 (  557)
  hydrogen bonds       : angle       6.99577 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 376
  time to evaluate  : 0.402 
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   14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7405 (m110)
REVERT: A  165 MET cc_start: 0.8984 (mmm) cc_final: 0.8551 (mpp)
REVERT: A  370 SER cc_start: 0.9131 (p) cc_final: 0.8818 (t)
REVERT: A  397 GLN cc_start: 0.8925 (mp10) cc_final: 0.8443 (mp10)
REVERT: A  415 ILE cc_start: 0.7030 (mm) cc_final: 0.6711 (mm)
REVERT: A  428 PHE cc_start: 0.9116 (t80) cc_final: 0.8820 (t80)
REVERT: A  446 MET cc_start: 0.8927 (tpt) cc_final: 0.8697 (tpp)
REVERT: A  512 LYS cc_start: 0.9126 (tttp) cc_final: 0.8792 (ttmm)
REVERT: A  521 MET cc_start: 0.7941 (mmt) cc_final: 0.7468 (mmt)
REVERT: A  574 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0)
REVERT: A  581 LEU cc_start: 0.8919 (mt) cc_final: 0.8698 (mt)
REVERT: A  589 MET cc_start: 0.8155 (mmm) cc_final: 0.7795 (mmm)
REVERT: A  612 VAL cc_start: 0.8839 (t) cc_final: 0.8499 (p)
REVERT: A  682 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7957 (mtm-85)
REVERT: A  709 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: A  712 TYR cc_start: 0.8591 (m-80) cc_final: 0.8236 (m-80)
REVERT: B   14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7390 (m110)
REVERT: B  165 MET cc_start: 0.8986 (mmm) cc_final: 0.8564 (mpp)
REVERT: B  303 LYS cc_start: 0.7984 (mttt) cc_final: 0.7779 (mttt)
REVERT: B  378 MET cc_start: 0.8575 (mmt) cc_final: 0.8103 (mmt)
REVERT: B  397 GLN cc_start: 0.8824 (mp10) cc_final: 0.8383 (mp10)
REVERT: B  446 MET cc_start: 0.8921 (tpt) cc_final: 0.8697 (tpt)
REVERT: B  448 MET cc_start: 0.8808 (ttt) cc_final: 0.8244 (ttt)
REVERT: B  459 SER cc_start: 0.8685 (m) cc_final: 0.8211 (t)
REVERT: B  521 MET cc_start: 0.7893 (mmt) cc_final: 0.7396 (mmt)
REVERT: B  589 MET cc_start: 0.8254 (mmm) cc_final: 0.7968 (mmm)
REVERT: B  645 LEU cc_start: 0.8316 (mt) cc_final: 0.8105 (mm)
REVERT: B  690 MET cc_start: 0.8038 (ttm) cc_final: 0.7739 (ttm)
REVERT: B  709 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: B  712 TYR cc_start: 0.8705 (m-80) cc_final: 0.8406 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 379
  average time/residue: 0.0992
  time to fit residues: 53.5730
Evaluate side-chains
  268 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 262
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 232 HIS
A 340 GLN
A 489 GLN
A 542 HIS
A 607 HIS
A 608 GLN
B 151 ASN
B 232 HIS
B 340 GLN
B 489 GLN
B 495 ASN
B 567 ASN
B 607 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.142190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113909 restraints weight = 18584.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.117144 restraints weight = 9920.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.119178 restraints weight = 6736.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.120313 restraints weight = 5322.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.121158 restraints weight = 4656.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11272  Z= 0.164
  Angle     :  0.729   8.023  15348  Z= 0.382
  Chirality :  0.046   0.171   1744
  Planarity :  0.006   0.058   1914
  Dihedral  :  7.321  49.908   1478
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 10.52 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.50 (0.20), residues: 1354
  helix: -1.48 (0.16), residues: 870
  sheet: -3.33 (1.05), residues: 30
  loop : -3.82 (0.24), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 698 
 TYR   0.023   0.002   TYR A 181 
 PHE   0.018   0.001   PHE B 428 
 TRP   0.027   0.002   TRP B 624 
 HIS   0.006   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (11272)
  covalent geometry    : angle       0.72861 (15348)
  hydrogen bonds       : bond        0.04101 (  557)
  hydrogen bonds       : angle       4.51561 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 311
  time to evaluate  : 0.425 
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   14 ASN cc_start: 0.7975 (m-40) cc_final: 0.7561 (m110)
REVERT: A   36 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7825 (mmt180)
REVERT: A  257 ASN cc_start: 0.8783 (m-40) cc_final: 0.8491 (m110)
REVERT: A  307 LYS cc_start: 0.8606 (mttt) cc_final: 0.8031 (mttt)
REVERT: A  370 SER cc_start: 0.8927 (p) cc_final: 0.8621 (t)
REVERT: A  415 ILE cc_start: 0.6725 (mm) cc_final: 0.6479 (mm)
REVERT: A  436 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8729 (mm)
REVERT: A  446 MET cc_start: 0.9121 (tpt) cc_final: 0.8671 (tpp)
REVERT: A  463 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.8183 (ttm-80)
REVERT: A  488 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8181 (mt-10)
REVERT: A  512 LYS cc_start: 0.9106 (tttp) cc_final: 0.8890 (ttmm)
REVERT: A  613 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.7113 (m-10)
REVERT: A  712 TYR cc_start: 0.8518 (m-80) cc_final: 0.8146 (m-80)
REVERT: B   36 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7965 (mmt-90)
REVERT: B  103 TRP cc_start: 0.7856 (t-100) cc_final: 0.7552 (t-100)
REVERT: B  182 GLU cc_start: 0.8167 (tt0) cc_final: 0.7912 (tt0)
REVERT: B  204 VAL cc_start: 0.9574 (t) cc_final: 0.9332 (m)
REVERT: B  257 ASN cc_start: 0.8741 (m-40) cc_final: 0.8468 (m110)
REVERT: B  307 LYS cc_start: 0.8521 (mttt) cc_final: 0.7661 (mttt)
REVERT: B  422 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8201 (ttpt)
REVERT: B  446 MET cc_start: 0.9066 (tpt) cc_final: 0.8599 (tpp)
REVERT: B  459 SER cc_start: 0.8576 (m) cc_final: 0.8229 (t)
REVERT: B  712 TYR cc_start: 0.8581 (m-80) cc_final: 0.8195 (m-80)
  outliers start: 41
  outliers final: 28
  residues processed: 334
  average time/residue: 0.0990
  time to fit residues: 47.3104
Evaluate side-chains
  297 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 267
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  492 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  632 ILE
Chi-restraints excluded: chain B residue  670 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 104 optimal weight:    6.9990
   chunk 127 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 340 GLN
A 567 ASN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
B 340 GLN
B 567 ASN
B 710 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.113398 restraints weight = 18659.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.116656 restraints weight = 9870.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.118722 restraints weight = 6639.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.120015 restraints weight = 5204.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.120798 restraints weight = 4495.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.136
  Angle     :  0.663   8.138  15348  Z= 0.347
  Chirality :  0.044   0.172   1744
  Planarity :  0.005   0.058   1914
  Dihedral  :  6.821  53.647   1478
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.38 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 14.83 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.63 (0.22), residues: 1354
  helix: -0.77 (0.17), residues: 894
  sheet: -3.10 (1.11), residues: 30
  loop : -3.67 (0.26), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 698 
 TYR   0.017   0.002   TYR A 181 
 PHE   0.020   0.001   PHE B 428 
 TRP   0.022   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (11272)
  covalent geometry    : angle       0.66281 (15348)
  hydrogen bonds       : bond        0.03473 (  557)
  hydrogen bonds       : angle       4.05171 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 283
  time to evaluate  : 0.321 
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   36 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7683 (tpp80)
REVERT: A   78 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: A  200 ASP cc_start: 0.8045 (t0) cc_final: 0.7825 (t0)
REVERT: A  257 ASN cc_start: 0.8707 (m-40) cc_final: 0.8458 (m110)
REVERT: A  303 LYS cc_start: 0.9082 (tptp) cc_final: 0.8844 (tptp)
REVERT: A  415 ILE cc_start: 0.6526 (mm) cc_final: 0.6120 (mm)
REVERT: A  421 MET cc_start: 0.8420 (mmt) cc_final: 0.8063 (mmt)
REVERT: A  446 MET cc_start: 0.9125 (tpt) cc_final: 0.8623 (tpp)
REVERT: A  459 SER cc_start: 0.8606 (m) cc_final: 0.8259 (t)
REVERT: A  531 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7888 (tm-30)
REVERT: A  570 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8696 (tm-30)
REVERT: A  613 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.6936 (m-10)
REVERT: A  712 TYR cc_start: 0.8564 (m-80) cc_final: 0.8198 (m-80)
REVERT: B   78 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7435 (tm-30)
REVERT: B  103 TRP cc_start: 0.7828 (t-100) cc_final: 0.7596 (t-100)
REVERT: B  182 GLU cc_start: 0.8145 (tt0) cc_final: 0.7871 (tt0)
REVERT: B  303 LYS cc_start: 0.9024 (tptp) cc_final: 0.8780 (tptp)
REVERT: B  415 ILE cc_start: 0.6391 (mm) cc_final: 0.5932 (mm)
REVERT: B  421 MET cc_start: 0.8050 (tpp) cc_final: 0.7673 (mmt)
REVERT: B  422 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8206 (ttpt)
REVERT: B  446 MET cc_start: 0.9097 (tpt) cc_final: 0.8629 (tpp)
REVERT: B  459 SER cc_start: 0.8625 (m) cc_final: 0.8253 (t)
REVERT: B  505 ILE cc_start: 0.8500 (tt) cc_final: 0.8279 (tt)
REVERT: B  531 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8389 (tm-30)
REVERT: B  613 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7090 (m-10)
REVERT: B  702 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6062 (mm)
REVERT: B  712 TYR cc_start: 0.8602 (m-80) cc_final: 0.8233 (m-80)
  outliers start: 42
  outliers final: 22
  residues processed: 304
  average time/residue: 0.0894
  time to fit residues: 39.8736
Evaluate side-chains
  284 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 257
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 111 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 132 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 75 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 567 ASN
** A 608 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 = 0.3651 r_free = 0.3651 target = 0.141769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.114408 restraints weight = 18639.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.117617 restraints weight = 9873.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.119681 restraints weight = 6642.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120984 restraints weight = 5191.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121646 restraints weight = 4464.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.126
  Angle     :  0.645   8.108  15348  Z= 0.332
  Chirality :  0.044   0.169   1744
  Planarity :  0.005   0.047   1914
  Dihedral  :  6.528  56.439   1478
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.29 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.96 (0.23), residues: 1354
  helix: -0.23 (0.17), residues: 888
  sheet: -2.88 (1.11), residues: 30
  loop : -3.42 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 698 
 TYR   0.015   0.002   TYR A 468 
 PHE   0.023   0.001   PHE A 428 
 TRP   0.022   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (11272)
  covalent geometry    : angle       0.64528 (15348)
  hydrogen bonds       : bond        0.03133 (  557)
  hydrogen bonds       : angle       3.85568 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 278
  time to evaluate  : 0.283 
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: A   36 ARG cc_start: 0.8287 (tpp-160) cc_final: 0.7580 (tpp80)
REVERT: A   78 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7469 (tm-30)
REVERT: A  190 GLN cc_start: 0.8269 (tp40) cc_final: 0.7977 (tp40)
REVERT: A  257 ASN cc_start: 0.8678 (m-40) cc_final: 0.8450 (m110)
REVERT: A  299 ASP cc_start: 0.6489 (m-30) cc_final: 0.6286 (t0)
REVERT: A  397 GLN cc_start: 0.8954 (mp10) cc_final: 0.8706 (mm-40)
REVERT: A  403 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8157 (mp0)
REVERT: A  421 MET cc_start: 0.8360 (mmt) cc_final: 0.8079 (tpp)
REVERT: A  446 MET cc_start: 0.9155 (tpt) cc_final: 0.8684 (tpp)
REVERT: A  459 SER cc_start: 0.8633 (m) cc_final: 0.8254 (t)
REVERT: A  488 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7799 (mt-10)
REVERT: A  521 MET cc_start: 0.8937 (mmm) cc_final: 0.8603 (mmm)
REVERT: A  531 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8008 (tm-30)
REVERT: A  570 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8702 (tm-30)
REVERT: A  613 TYR cc_start: 0.9032 (OUTLIER) cc_final: 0.7166 (m-10)
REVERT: A  712 TYR cc_start: 0.8559 (m-80) cc_final: 0.8210 (m-80)
REVERT: B   14 ASN cc_start: 0.7653 (m110) cc_final: 0.7415 (m110)
REVERT: B   36 ARG cc_start: 0.8501 (tpp-160) cc_final: 0.8041 (tpp-160)
REVERT: B   78 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7387 (tm-30)
REVERT: B  182 GLU cc_start: 0.8212 (tt0) cc_final: 0.7946 (tt0)
REVERT: B  204 VAL cc_start: 0.9510 (t) cc_final: 0.9287 (m)
REVERT: B  299 ASP cc_start: 0.7052 (m-30) cc_final: 0.6809 (t0)
REVERT: B  446 MET cc_start: 0.9132 (tpt) cc_final: 0.8671 (tpp)
REVERT: B  459 SER cc_start: 0.8606 (m) cc_final: 0.8250 (t)
REVERT: B  488 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7557 (mt-10)
REVERT: B  512 LYS cc_start: 0.9103 (tttp) cc_final: 0.8302 (tttm)
REVERT: B  531 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8387 (tm-30)
REVERT: B  613 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.7066 (m-10)
REVERT: B  712 TYR cc_start: 0.8589 (m-80) cc_final: 0.8213 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 299
  average time/residue: 0.0887
  time to fit residues: 38.9592
Evaluate side-chains
  289 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 259
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  670 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 128 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 122 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
B 397 GLN
** B 574 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 = 0.3636 r_free = 0.3636 target = 0.140631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.112841 restraints weight = 18710.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115983 restraints weight = 10089.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.117986 restraints weight = 6849.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119224 restraints weight = 5403.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.119887 restraints weight = 4678.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.129
  Angle     :  0.642   8.449  15348  Z= 0.329
  Chirality :  0.043   0.161   1744
  Planarity :  0.005   0.043   1914
  Dihedral  :  6.334  59.095   1478
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 16.98 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.23), residues: 1354
  helix:  0.13 (0.18), residues: 890
  sheet: -2.95 (1.06), residues: 30
  loop : -3.27 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 698 
 TYR   0.014   0.002   TYR A 468 
 PHE   0.024   0.001   PHE A 428 
 TRP   0.022   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11272)
  covalent geometry    : angle       0.64161 (15348)
  hydrogen bonds       : bond        0.03106 (  557)
  hydrogen bonds       : angle       3.76677 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 262
  time to evaluate  : 0.393 
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: A   14 ASN cc_start: 0.8042 (m-40) cc_final: 0.7797 (m110)
REVERT: A   36 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.7643 (tpp80)
REVERT: A   47 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6833 (pp)
REVERT: A   78 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7449 (tm-30)
REVERT: A  190 GLN cc_start: 0.8309 (tp40) cc_final: 0.7975 (tp40)
REVERT: A  257 ASN cc_start: 0.8658 (m-40) cc_final: 0.8458 (m110)
REVERT: A  299 ASP cc_start: 0.6943 (m-30) cc_final: 0.6715 (t0)
REVERT: A  307 LYS cc_start: 0.8464 (mttt) cc_final: 0.8182 (ttmt)
REVERT: A  403 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8165 (mp0)
REVERT: A  421 MET cc_start: 0.8393 (mmt) cc_final: 0.8191 (mmt)
REVERT: A  446 MET cc_start: 0.9176 (tpt) cc_final: 0.8756 (tpp)
REVERT: A  459 SER cc_start: 0.8667 (m) cc_final: 0.8306 (t)
REVERT: A  488 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: A  531 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8075 (tm-30)
REVERT: A  570 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8848 (tm-30)
REVERT: A  591 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8745 (mp)
REVERT: A  613 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7052 (m-10)
REVERT: A  712 TYR cc_start: 0.8586 (m-80) cc_final: 0.8211 (m-80)
REVERT: B   14 ASN cc_start: 0.7767 (m110) cc_final: 0.7500 (m110)
REVERT: B   36 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8178 (tpp80)
REVERT: B   78 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7384 (tm-30)
REVERT: B  126 THR cc_start: 0.8166 (p) cc_final: 0.7916 (t)
REVERT: B  182 GLU cc_start: 0.8190 (tt0) cc_final: 0.7925 (tt0)
REVERT: B  299 ASP cc_start: 0.7041 (m-30) cc_final: 0.6816 (t0)
REVERT: B  446 MET cc_start: 0.9176 (tpt) cc_final: 0.8752 (tpp)
REVERT: B  448 MET cc_start: 0.8566 (ttp) cc_final: 0.7457 (ttp)
REVERT: B  459 SER cc_start: 0.8666 (m) cc_final: 0.8282 (t)
REVERT: B  488 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7721 (mt-10)
REVERT: B  531 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8191 (tm-30)
REVERT: B  613 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.6954 (m-10)
REVERT: B  702 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6226 (mm)
REVERT: B  712 TYR cc_start: 0.8608 (m-80) cc_final: 0.8190 (m-80)
  outliers start: 50
  outliers final: 30
  residues processed: 289
  average time/residue: 0.0859
  time to fit residues: 37.2940
Evaluate side-chains
  284 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 123 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 114 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0980
   chunk 36 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.140472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.112869 restraints weight = 18684.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.116074 restraints weight = 9959.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.118087 restraints weight = 6694.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.119350 restraints weight = 5238.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.120025 restraints weight = 4521.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11272  Z= 0.122
  Angle     :  0.649   8.471  15348  Z= 0.328
  Chirality :  0.043   0.158   1744
  Planarity :  0.005   0.043   1914
  Dihedral  :  6.156  57.609   1478
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 18.62 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.24), residues: 1354
  helix:  0.35 (0.18), residues: 892
  sheet: -2.90 (1.05), residues: 30
  loop : -3.22 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 698 
 TYR   0.012   0.001   TYR A 468 
 PHE   0.025   0.001   PHE A 428 
 TRP   0.019   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11272)
  covalent geometry    : angle       0.64851 (15348)
  hydrogen bonds       : bond        0.02979 (  557)
  hydrogen bonds       : angle       3.72317 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 259
  time to evaluate  : 0.426 
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: A   14 ASN cc_start: 0.8033 (m-40) cc_final: 0.7681 (m110)
REVERT: A   36 ARG cc_start: 0.8343 (tpp-160) cc_final: 0.7644 (tpp80)
REVERT: A   47 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6839 (pp)
REVERT: A   78 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7407 (tm-30)
REVERT: A  190 GLN cc_start: 0.8315 (tp40) cc_final: 0.7930 (tp40)
REVERT: A  299 ASP cc_start: 0.6944 (m-30) cc_final: 0.6730 (t0)
REVERT: A  307 LYS cc_start: 0.8438 (mttt) cc_final: 0.8214 (ttmt)
REVERT: A  403 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8133 (mp0)
REVERT: A  436 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8534 (mm)
REVERT: A  446 MET cc_start: 0.9153 (tpt) cc_final: 0.8738 (tpp)
REVERT: A  459 SER cc_start: 0.8653 (m) cc_final: 0.8282 (t)
REVERT: A  488 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7546 (mt-10)
REVERT: A  521 MET cc_start: 0.9053 (mmm) cc_final: 0.8795 (mmm)
REVERT: A  531 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8131 (tm-30)
REVERT: A  570 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8854 (tm-30)
REVERT: A  591 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8704 (mp)
REVERT: A  613 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7025 (m-10)
REVERT: A  712 TYR cc_start: 0.8627 (m-80) cc_final: 0.8202 (m-80)
REVERT: B   14 ASN cc_start: 0.7828 (m110) cc_final: 0.7497 (m110)
REVERT: B   47 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6943 (pp)
REVERT: B   78 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7312 (tm-30)
REVERT: B  378 MET cc_start: 0.7622 (mmm) cc_final: 0.7279 (mmt)
REVERT: B  421 MET cc_start: 0.8091 (tpp) cc_final: 0.7766 (mmt)
REVERT: B  446 MET cc_start: 0.9192 (tpt) cc_final: 0.8745 (tpp)
REVERT: B  448 MET cc_start: 0.8406 (ttp) cc_final: 0.8145 (ttp)
REVERT: B  459 SER cc_start: 0.8664 (m) cc_final: 0.8271 (t)
REVERT: B  488 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7845 (mt-10)
REVERT: B  521 MET cc_start: 0.9054 (mmp) cc_final: 0.8830 (mmm)
REVERT: B  531 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8223 (tm-30)
REVERT: B  613 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.6935 (m-10)
REVERT: B  702 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6195 (mm)
REVERT: B  712 TYR cc_start: 0.8586 (m-80) cc_final: 0.8177 (m-80)
  outliers start: 46
  outliers final: 30
  residues processed: 288
  average time/residue: 0.0818
  time to fit residues: 36.3717
Evaluate side-chains
  282 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 242
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 109 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 129 optimal weight:    0.0370
   chunk 90 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 162 HIS
A 257 ASN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.144731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.117046 restraints weight = 18521.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120304 restraints weight = 9913.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.122351 restraints weight = 6673.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.123610 restraints weight = 5232.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124153 restraints weight = 4527.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11272  Z= 0.116
  Angle     :  0.625   7.020  15348  Z= 0.318
  Chirality :  0.043   0.159   1744
  Planarity :  0.005   0.043   1914
  Dihedral  :  5.884  51.996   1478
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 19.91 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.24), residues: 1354
  helix:  0.52 (0.18), residues: 892
  sheet: -2.86 (1.05), residues: 30
  loop : -3.17 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 698 
 TYR   0.013   0.001   TYR A 468 
 PHE   0.025   0.001   PHE A 428 
 TRP   0.018   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11272)
  covalent geometry    : angle       0.62471 (15348)
  hydrogen bonds       : bond        0.02909 (  557)
  hydrogen bonds       : angle       3.70047 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 264
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.7586 (tpp80)
REVERT: A   47 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6899 (pp)
REVERT: A  162 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7571 (m90)
REVERT: A  307 LYS cc_start: 0.8399 (mttt) cc_final: 0.8158 (ttmt)
REVERT: A  403 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8133 (mp0)
REVERT: A  436 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8488 (mm)
REVERT: A  446 MET cc_start: 0.9082 (tpt) cc_final: 0.8657 (tpp)
REVERT: A  459 SER cc_start: 0.8622 (m) cc_final: 0.8207 (t)
REVERT: A  488 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7636 (mt-10)
REVERT: A  531 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8123 (tm-30)
REVERT: A  570 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8843 (tm-30)
REVERT: A  613 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7077 (m-10)
REVERT: A  712 TYR cc_start: 0.8612 (m-80) cc_final: 0.8196 (m-80)
REVERT: B   14 ASN cc_start: 0.7917 (m110) cc_final: 0.7563 (m110)
REVERT: B   36 ARG cc_start: 0.8583 (tpp-160) cc_final: 0.7872 (tpp80)
REVERT: B   47 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6943 (pp)
REVERT: B  420 PHE cc_start: 0.7404 (t80) cc_final: 0.6902 (m-10)
REVERT: B  421 MET cc_start: 0.8060 (tpp) cc_final: 0.7776 (mmt)
REVERT: B  446 MET cc_start: 0.9202 (tpt) cc_final: 0.8747 (tpp)
REVERT: B  459 SER cc_start: 0.8613 (m) cc_final: 0.8224 (t)
REVERT: B  488 GLU cc_start: 0.8173 (mt-10) cc_final: 0.6916 (mt-10)
REVERT: B  512 LYS cc_start: 0.8969 (tttp) cc_final: 0.8215 (tttp)
REVERT: B  531 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8194 (tm-30)
REVERT: B  613 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.7285 (m-10)
REVERT: B  702 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6110 (mm)
REVERT: B  712 TYR cc_start: 0.8611 (m-80) cc_final: 0.8182 (m-80)
  outliers start: 47
  outliers final: 30
  residues processed: 294
  average time/residue: 0.0820
  time to fit residues: 36.3896
Evaluate side-chains
  281 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 241
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  162 HIS
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 132 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0170
   overall best weight:    0.6222

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 608 GLN
B 151 ASN
** B 574 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 = 0.3684 r_free = 0.3684 target = 0.144448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.116947 restraints weight = 18472.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.120213 restraints weight = 9911.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.122276 restraints weight = 6684.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.123550 restraints weight = 5258.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124250 restraints weight = 4547.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11272  Z= 0.121
  Angle     :  0.646   7.930  15348  Z= 0.327
  Chirality :  0.043   0.162   1744
  Planarity :  0.005   0.044   1914
  Dihedral  :  5.801  48.384   1478
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.81 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.24), residues: 1354
  helix:  0.64 (0.18), residues: 890
  sheet: -2.79 (1.06), residues: 30
  loop : -3.13 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 698 
 TYR   0.014   0.001   TYR A 468 
 PHE   0.027   0.001   PHE A 428 
 TRP   0.016   0.001   TRP A 525 
 HIS   0.017   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11272)
  covalent geometry    : angle       0.64562 (15348)
  hydrogen bonds       : bond        0.02876 (  557)
  hydrogen bonds       : angle       3.73713 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 251
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7810 (m110) cc_final: 0.7574 (m110)
REVERT: A   36 ARG cc_start: 0.8358 (tpp-160) cc_final: 0.7618 (tpp80)
REVERT: A   47 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6913 (pp)
REVERT: A  126 THR cc_start: 0.7860 (p) cc_final: 0.7651 (t)
REVERT: A  161 THR cc_start: 0.8113 (p) cc_final: 0.7753 (t)
REVERT: A  378 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (mmm)
REVERT: A  403 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8132 (mp0)
REVERT: A  436 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8497 (mm)
REVERT: A  446 MET cc_start: 0.9105 (tpt) cc_final: 0.8630 (tpp)
REVERT: A  459 SER cc_start: 0.8584 (m) cc_final: 0.8214 (t)
REVERT: A  488 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7575 (mt-10)
REVERT: A  531 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8170 (tm-30)
REVERT: A  570 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8883 (tm-30)
REVERT: A  613 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7053 (m-10)
REVERT: A  643 MET cc_start: 0.8011 (tpp) cc_final: 0.7659 (mtt)
REVERT: A  712 TYR cc_start: 0.8630 (m-80) cc_final: 0.8199 (m-80)
REVERT: B   36 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.7877 (tpp80)
REVERT: B   47 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6964 (pp)
REVERT: B  378 MET cc_start: 0.8035 (mmt) cc_final: 0.7822 (mmt)
REVERT: B  420 PHE cc_start: 0.7376 (t80) cc_final: 0.6894 (m-10)
REVERT: B  421 MET cc_start: 0.8121 (tpp) cc_final: 0.7834 (mmt)
REVERT: B  446 MET cc_start: 0.9225 (tpt) cc_final: 0.8739 (tpp)
REVERT: B  459 SER cc_start: 0.8688 (m) cc_final: 0.8331 (t)
REVERT: B  488 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: B  512 LYS cc_start: 0.8982 (tttp) cc_final: 0.8445 (tttm)
REVERT: B  521 MET cc_start: 0.8772 (mmp) cc_final: 0.8303 (mmm)
REVERT: B  531 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8194 (tm-30)
REVERT: B  576 TYR cc_start: 0.8368 (m-80) cc_final: 0.8088 (m-80)
REVERT: B  613 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7355 (m-10)
REVERT: B  702 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6093 (mm)
REVERT: B  712 TYR cc_start: 0.8686 (m-80) cc_final: 0.8258 (m-80)
  outliers start: 44
  outliers final: 32
  residues processed: 281
  average time/residue: 0.0760
  time to fit residues: 32.6196
Evaluate side-chains
  281 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 239
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  661 LEU
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 116 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:   10.0000
   chunk 5 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 125 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117462 restraints weight = 18523.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.120682 restraints weight = 9961.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122736 restraints weight = 6772.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123885 restraints weight = 5336.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.124706 restraints weight = 4661.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.125
  Angle     :  0.656   9.950  15348  Z= 0.331
  Chirality :  0.044   0.162   1744
  Planarity :  0.005   0.044   1914
  Dihedral  :  5.638  43.414   1478
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 21.72 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.24), residues: 1354
  helix:  0.74 (0.18), residues: 890
  sheet: -2.73 (1.08), residues: 30
  loop : -3.05 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 698 
 TYR   0.014   0.001   TYR A 468 
 PHE   0.033   0.001   PHE B 428 
 TRP   0.016   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11272)
  covalent geometry    : angle       0.65629 (15348)
  hydrogen bonds       : bond        0.02926 (  557)
  hydrogen bonds       : angle       3.76703 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 244
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7798 (m110) cc_final: 0.7565 (m110)
REVERT: A   36 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.7626 (tpp80)
REVERT: A   47 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6897 (pp)
REVERT: A  370 SER cc_start: 0.8923 (p) cc_final: 0.8687 (t)
REVERT: A  403 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8073 (mp0)
REVERT: A  436 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8489 (mm)
REVERT: A  446 MET cc_start: 0.9043 (tpt) cc_final: 0.8618 (tpp)
REVERT: A  448 MET cc_start: 0.8651 (ttp) cc_final: 0.8363 (ttp)
REVERT: A  459 SER cc_start: 0.8630 (m) cc_final: 0.8333 (t)
REVERT: A  488 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7181 (mt-10)
REVERT: A  512 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8426 (tppp)
REVERT: A  570 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8908 (tm-30)
REVERT: A  608 GLN cc_start: 0.8575 (mm110) cc_final: 0.7996 (mm-40)
REVERT: A  613 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7138 (m-10)
REVERT: A  643 MET cc_start: 0.7983 (tpp) cc_final: 0.7662 (mtt)
REVERT: A  712 TYR cc_start: 0.8658 (m-80) cc_final: 0.8193 (m-80)
REVERT: B   36 ARG cc_start: 0.8602 (tpp-160) cc_final: 0.7887 (tpp80)
REVERT: B   47 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6996 (pp)
REVERT: B  420 PHE cc_start: 0.7368 (t80) cc_final: 0.6887 (m-10)
REVERT: B  421 MET cc_start: 0.8108 (tpp) cc_final: 0.7808 (mmt)
REVERT: B  446 MET cc_start: 0.9196 (tpt) cc_final: 0.8711 (tpp)
REVERT: B  459 SER cc_start: 0.8698 (m) cc_final: 0.8354 (t)
REVERT: B  488 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7700 (mt-10)
REVERT: B  512 LYS cc_start: 0.8998 (tttp) cc_final: 0.8510 (tttm)
REVERT: B  521 MET cc_start: 0.9026 (mmp) cc_final: 0.8373 (mmm)
REVERT: B  531 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (tm-30)
REVERT: B  613 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.7415 (m-10)
REVERT: B  643 MET cc_start: 0.8155 (tpp) cc_final: 0.7753 (mtt)
REVERT: B  702 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5775 (mm)
REVERT: B  712 TYR cc_start: 0.8686 (m-80) cc_final: 0.8258 (m-80)
  outliers start: 43
  outliers final: 30
  residues processed: 272
  average time/residue: 0.0760
  time to fit residues: 31.5905
Evaluate side-chains
  277 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 239
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0570
   chunk 52 optimal weight:    9.9990
   chunk 30 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
B 151 ASN
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 615 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 = 0.3693 r_free = 0.3693 target = 0.145148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117477 restraints weight = 18601.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120713 restraints weight = 9989.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.122745 restraints weight = 6767.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.123928 restraints weight = 5343.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.124720 restraints weight = 4656.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.4365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11272  Z= 0.126
  Angle     :  0.664  12.258  15348  Z= 0.336
  Chirality :  0.044   0.164   1744
  Planarity :  0.005   0.046   1914
  Dihedral  :  5.389  40.977   1473
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.59 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.24), residues: 1354
  helix:  0.78 (0.18), residues: 900
  sheet: -2.67 (1.09), residues: 30
  loop : -2.97 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 698 
 TYR   0.016   0.001   TYR A 468 
 PHE   0.031   0.001   PHE B 428 
 TRP   0.015   0.001   TRP A 525 
 HIS   0.006   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (11272)
  covalent geometry    : angle       0.66401 (15348)
  hydrogen bonds       : bond        0.02939 (  557)
  hydrogen bonds       : angle       3.80066 ( 1653)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7851 (m110) cc_final: 0.7627 (m110)
REVERT: A   36 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.7621 (tpp80)
REVERT: A   47 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6896 (pp)
REVERT: A  370 SER cc_start: 0.8917 (p) cc_final: 0.8678 (t)
REVERT: A  403 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8071 (mp0)
REVERT: A  436 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8488 (mm)
REVERT: A  446 MET cc_start: 0.9060 (tpt) cc_final: 0.8523 (tpt)
REVERT: A  459 SER cc_start: 0.8619 (m) cc_final: 0.8314 (t)
REVERT: A  488 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7285 (mt-10)
REVERT: A  512 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8238 (tppp)
REVERT: A  570 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8890 (tm-30)
REVERT: A  608 GLN cc_start: 0.8723 (mm110) cc_final: 0.8162 (mm-40)
REVERT: A  613 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7128 (m-10)
REVERT: A  643 MET cc_start: 0.7966 (tpp) cc_final: 0.7681 (mtt)
REVERT: A  712 TYR cc_start: 0.8694 (m-80) cc_final: 0.8178 (m-80)
REVERT: B   36 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.7883 (tpp80)
REVERT: B   47 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7010 (pp)
REVERT: B   86 GLU cc_start: 0.8391 (tp30) cc_final: 0.8175 (tp30)
REVERT: B  421 MET cc_start: 0.8108 (tpp) cc_final: 0.7803 (mmt)
REVERT: B  446 MET cc_start: 0.9201 (tpt) cc_final: 0.8686 (tpp)
REVERT: B  459 SER cc_start: 0.8693 (m) cc_final: 0.8344 (t)
REVERT: B  488 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7914 (mt-10)
REVERT: B  521 MET cc_start: 0.9000 (mmp) cc_final: 0.8482 (mmm)
REVERT: B  531 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7999 (tm-30)
REVERT: B  574 GLN cc_start: 0.8323 (mt0) cc_final: 0.8104 (mt0)
REVERT: B  613 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7400 (m-10)
REVERT: B  643 MET cc_start: 0.8127 (tpp) cc_final: 0.7885 (mtt)
REVERT: B  702 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5689 (mm)
REVERT: B  712 TYR cc_start: 0.8685 (m-80) cc_final: 0.8255 (m-80)
  outliers start: 39
  outliers final: 27
  residues processed: 272
  average time/residue: 0.0768
  time to fit residues: 31.9056
Evaluate side-chains
  278 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 243
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  403 GLU
Chi-restraints excluded: chain A residue  422 LYS
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  702 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  702 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 98 optimal weight:    0.0870
   chunk 120 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0770
   chunk 32 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 96 optimal weight:    9.9990
   chunk 107 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.146562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.118967 restraints weight = 18412.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.122302 restraints weight = 9665.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124364 restraints weight = 6467.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125617 restraints weight = 5077.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.126303 restraints weight = 4402.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.124
  Angle     :  0.657   9.096  15348  Z= 0.331
  Chirality :  0.043   0.161   1744
  Planarity :  0.005   0.046   1914
  Dihedral  :  5.181  40.742   1471
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.41 %
    Favored  : 74.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.24), residues: 1354
  helix:  0.82 (0.18), residues: 900
  sheet: -2.65 (1.09), residues: 30
  loop : -2.93 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 698 
 TYR   0.015   0.001   TYR B 576 
 PHE   0.031   0.001   PHE B 428 
 TRP   0.017   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (11272)
  covalent geometry    : angle       0.65680 (15348)
  hydrogen bonds       : bond        0.02919 (  557)
  hydrogen bonds       : angle       3.78926 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1752.46 seconds
wall clock time: 30 minutes 57.10 seconds (1857.10 seconds total)