Starting phenix.real_space_refine
on Wed Mar  4 02:38:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ui6_26540/03_2026/7ui6_26540.cif"
  }
  resolution = 3.7
  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=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     S      52      5.16       5
     C    6568      2.51       5
     N    1736      2.21       5
     O    1788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 10148
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 609, 5072
          Classifications: {'peptide': 609}
          Link IDs: {'PTRANS': 23, 'TRANS': 585}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 609, 5072
          Classifications: {'peptide': 609}
          Link IDs: {'PTRANS': 23, 'TRANS': 585}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.65, per 1000 atoms: 0.26
  Number of scatterers: 10148
  At special positions: 0
  Unit cell: (106.6, 113.012, 113.012, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      4     24.99
     S      52     16.00
     O    1788      8.00
     N    1736      7.00
     C    6568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 354 " - pdb=" SG  CYS A 369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 726 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 354 " - pdb=" SG  CYS B 369 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 726 " distance=2.03

  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: 0.78
  Conformation dependent library (CDL) restraints added in 468.7 milliseconds
  

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 8 sheets defined
      48.4% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 145 through 163
      removed outlier: 4.064A  pdb=" N   ALA A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   HIS A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 190
      removed outlier: 3.660A  pdb=" N   THR A 184 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   MET A 190 " --> pdb=" O   PHE A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 225
      removed outlier: 3.606A  pdb=" N   LYS A 224 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 250 through 256
      removed outlier: 4.162A  pdb=" N   LEU A 254 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 260
    Processing helix  chain 'A' and resid 305 through 310
      removed outlier: 4.020A  pdb=" N   LYS A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 323
      removed outlier: 3.635A  pdb=" N   MET A 315 " --> pdb=" O   LYS A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 345
      removed outlier: 3.712A  pdb=" N   ASN A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ALA A 340 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 357
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.994A  pdb=" N   CYS A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 389
    Processing helix  chain 'A' and resid 393 through 406
      removed outlier: 3.822A  pdb=" N   PHE A 397 " --> pdb=" O   HIS A 393 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   PHE A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 405 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 412
    Processing helix  chain 'A' and resid 427 through 435
    Processing helix  chain 'A' and resid 443 through 452
      removed outlier: 3.695A  pdb=" N   PHE A 451 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 452 " --> pdb=" O   ARG A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 486
      No H-bonds generated for 'chain 'A' and resid 484 through 486'
    Processing helix  chain 'A' and resid 487 through 495
    Processing helix  chain 'A' and resid 506 through 520
    Processing helix  chain 'A' and resid 520 through 526
      removed outlier: 3.962A  pdb=" N   MET A 524 " --> pdb=" O   SER A 520 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 553
      removed outlier: 3.880A  pdb=" N   HIS A 553 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 584
    Processing helix  chain 'A' and resid 609 through 620
    Processing helix  chain 'A' and resid 630 through 637
      removed outlier: 3.524A  pdb=" N   GLY A 633 " --> pdb=" O   TRP A 630 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   HIS A 634 " --> pdb=" O   THR A 631 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA A 635 " --> pdb=" O   LYS A 632 " (cutoff:3.500A)
      Proline residue:  A 636  - end of helix
      No H-bonds generated for 'chain 'A' and resid 630 through 637'
    Processing helix  chain 'A' and resid 638 through 644
      removed outlier: 3.606A  pdb=" N   TRP A 642 " --> pdb=" O   ASN A 638 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   THR A 644 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 691
      removed outlier: 3.620A  pdb=" N   GLN A 691 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 718
      removed outlier: 3.613A  pdb=" N   THR A 715 " --> pdb=" O   SER A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 743
      removed outlier: 4.090A  pdb=" N   ARG A 724 " --> pdb=" O   ASN A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 756
      removed outlier: 3.702A  pdb=" N   LEU A 747 " --> pdb=" O   GLY A 743 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   LYS A 748 " --> pdb=" O   PHE A 744 " (cutoff:3.500A)
      removed outlier: 4.851A  pdb=" N   TYR A 749 " --> pdb=" O   ALA A 745 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 750 " --> pdb=" O   ALA A 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 163
      removed outlier: 4.015A  pdb=" N   ALA B 149 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   THR B 155 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   HIS B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 190
    Processing helix  chain 'B' and resid 204 through 209
      removed outlier: 3.544A  pdb=" N   VAL B 208 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 226 through 231
    Processing helix  chain 'B' and resid 250 through 257
      removed outlier: 4.137A  pdb=" N   LEU B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 257 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 260
      No H-bonds generated for 'chain 'B' and resid 258 through 260'
    Processing helix  chain 'B' and resid 303 through 310
    Processing helix  chain 'B' and resid 311 through 323
      removed outlier: 4.024A  pdb=" N   MET B 315 " --> pdb=" O   LYS B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 345
      removed outlier: 3.609A  pdb=" N   ASN B 339 " --> pdb=" O   GLN B 335 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 357
      removed outlier: 3.556A  pdb=" N   ASN B 357 " --> pdb=" O   CYS B 354 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 370
      removed outlier: 3.644A  pdb=" N   TYR B 370 " --> pdb=" O   GLU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.940A  pdb=" N   VAL B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 406
      removed outlier: 3.664A  pdb=" N   PHE B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 412
    Processing helix  chain 'B' and resid 427 through 437
      removed outlier: 3.770A  pdb=" N   GLU B 436 " --> pdb=" O   LYS B 432 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU B 437 " --> pdb=" O   GLN B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 451
      removed outlier: 4.055A  pdb=" N   PHE B 451 " --> pdb=" O   ARG B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 485
      removed outlier: 3.695A  pdb=" N   ARG B 484 " --> pdb=" O   SER B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 495
      removed outlier: 4.431A  pdb=" N   ALA B 490 " --> pdb=" O   GLN B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 520
    Processing helix  chain 'B' and resid 520 through 526
      removed outlier: 3.538A  pdb=" N   ARG B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 553
      removed outlier: 3.829A  pdb=" N   HIS B 553 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 584
      removed outlier: 3.620A  pdb=" N   TYR B 575 " --> pdb=" O   GLY B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 619
    Processing helix  chain 'B' and resid 630 through 637
      removed outlier: 3.636A  pdb=" N   HIS B 634 " --> pdb=" O   THR B 631 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   ALA B 635 " --> pdb=" O   LYS B 632 " (cutoff:3.500A)
      Proline residue:  B 636  - end of helix
    Processing helix  chain 'B' and resid 638 through 643
      removed outlier: 3.922A  pdb=" N   TRP B 642 " --> pdb=" O   ASN B 638 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ARG B 643 " --> pdb=" O   PHE B 639 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 638 through 643'
    Processing helix  chain 'B' and resid 680 through 691
      removed outlier: 4.038A  pdb=" N   HIS B 684 " --> pdb=" O   ASN B 680 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN B 691 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 720
      removed outlier: 3.970A  pdb=" N   THR B 715 " --> pdb=" O   SER B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 720 through 743
      removed outlier: 3.545A  pdb=" N   ARG B 724 " --> pdb=" O   ASN B 720 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 743 through 756
      removed outlier: 3.676A  pdb=" N   LEU B 747 " --> pdb=" O   GLY B 743 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LYS B 748 " --> pdb=" O   PHE B 744 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   TYR B 749 " --> pdb=" O   ALA B 745 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU B 750 " --> pdb=" O   ALA B 746 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200
      removed outlier: 6.656A  pdb=" N   LEU A 168 " --> pdb=" O   ARG A 195 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   ASP A 197 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   PHE A 170 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   TYR A 199 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU A 172 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   LEU A 241 " --> pdb=" O   HIS A 139 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ALA A 141 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   VAL A 270 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   GLY A 298 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 11.244A  pdb=" N   GLY A 268 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   LEU A 267 " --> pdb=" O   TYR A 350 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247
      removed outlier: 3.783A  pdb=" N   ILE A 379 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457
      removed outlier: 3.528A  pdb=" N   ILE A 533 " --> pdb=" O   HIS A 457 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE A 499 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
      removed outlier: 7.896A  pdb=" N   HIS A 532 " --> pdb=" O   ILE A 499 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU A 501 " --> pdb=" O   HIS A 532 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   VAL A 534 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU A 503 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   SER A 500 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   LEU A 476 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ALA A 502 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ALA A 478 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   THR A 475 " --> pdb=" O   PHE A 560 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL A 661 " --> pdb=" O   LEU A 561 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   ARG A 664 " --> pdb=" O   LYS A 590 " (cutoff:3.500A)
      removed outlier: 9.169A  pdb=" N   LYS A 590 " --> pdb=" O   ARG A 664 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   PHE A 695 " --> pdb=" O   VAL A 651 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A 651 " --> pdb=" O   PHE A 695 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   TYR A 649 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 599
    Processing sheet with id=AA5, first strand: chain 'B' and resid 194 through 200
      removed outlier: 6.674A  pdb=" N   HIS B 139 " --> pdb=" O   ILE B 239 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   LEU B 241 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   ALA B 141 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 8.065A  pdb=" N   VAL B 299 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   VAL B 270 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU B 352 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   LEU B 269 " --> pdb=" O   LEU B 352 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 247
      removed outlier: 3.617A  pdb=" N   HIS B 380 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 456 through 457
      removed outlier: 3.555A  pdb=" N   ILE B 533 " --> pdb=" O   HIS B 457 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 474 through 477
      removed outlier: 6.093A  pdb=" N   THR B 475 " --> pdb=" O   PHE B 560 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL B 661 " --> pdb=" O   LEU B 561 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   TYR B 660 " --> pdb=" O   VAL B 594 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   ARG B 664 " --> pdb=" O   LYS B 590 " (cutoff:3.500A)
      removed outlier: 8.992A  pdb=" N   LYS B 590 " --> pdb=" O   ARG B 664 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ALA B 591 " --> pdb=" O   ILE B 696 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   PHE B 695 " --> pdb=" O   VAL B 651 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    978 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: 1.73

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1782
        1.32 -     1.45: 2884
        1.45 -     1.57: 5666
        1.57 -     1.70: 0
        1.70 -     1.82: 90
  Bond restraints: 10422
  Sorted by residual:
  bond pdb=" CA  SER B 500 "
       pdb=" CB  SER B 500 "
    ideal  model  delta    sigma   weight residual
    1.534  1.461  0.073 1.77e-02 3.19e+03 1.72e+01
  bond pdb=" N   ALA B 701 "
       pdb=" CA  ALA B 701 "
    ideal  model  delta    sigma   weight residual
    1.454  1.500 -0.045 1.16e-02 7.43e+03 1.53e+01
  bond pdb=" N   GLU B 598 "
       pdb=" CA  GLU B 598 "
    ideal  model  delta    sigma   weight residual
    1.455  1.500 -0.044 1.18e-02 7.18e+03 1.41e+01
  bond pdb=" C   ALA B 502 "
       pdb=" N   LEU B 503 "
    ideal  model  delta    sigma   weight residual
    1.331  1.285  0.046 1.29e-02 6.01e+03 1.26e+01
  bond pdb=" N   THR B 599 "
       pdb=" CA  THR B 599 "
    ideal  model  delta    sigma   weight residual
    1.454  1.499 -0.045 1.29e-02 6.01e+03 1.24e+01
  ... (remaining 10417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 13542
        2.16 -     4.31: 476
        4.31 -     6.47: 82
        6.47 -     8.63: 22
        8.63 -    10.79: 10
  Bond angle restraints: 14132
  Sorted by residual:
  angle pdb=" N   ASP A 305 "
        pdb=" CA  ASP A 305 "
        pdb=" C   ASP A 305 "
      ideal   model   delta    sigma   weight residual
     111.90  102.14    9.76 1.32e+00 5.74e-01 5.46e+01
  angle pdb=" N   PRO B 595 "
        pdb=" CA  PRO B 595 "
        pdb=" C   PRO B 595 "
      ideal   model   delta    sigma   weight residual
     110.50  121.01  -10.51 1.57e+00 4.06e-01 4.48e+01
  angle pdb=" C   PHE B 186 "
        pdb=" N   GLN B 187 "
        pdb=" CA  GLN B 187 "
      ideal   model   delta    sigma   weight residual
     120.38  112.92    7.46 1.46e+00 4.69e-01 2.61e+01
  angle pdb=" C   PHE B 566 "
        pdb=" N   LEU B 567 "
        pdb=" CA  LEU B 567 "
      ideal   model   delta    sigma   weight residual
     122.37  117.67    4.70 9.30e-01 1.16e+00 2.55e+01
  angle pdb=" C   THR B 184 "
        pdb=" N   LEU B 185 "
        pdb=" CA  LEU B 185 "
      ideal   model   delta    sigma   weight residual
     120.63  114.31    6.32 1.36e+00 5.41e-01 2.16e+01
  ... (remaining 14127 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 5440
       17.58 -    35.16: 589
       35.16 -    52.74: 120
       52.74 -    70.32: 28
       70.32 -    87.90: 9
  Dihedral angle restraints: 6186
    sinusoidal: 2554
      harmonic: 3632
  Sorted by residual:
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 726 "
           pdb=" CB  CYS B 726 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.18  -70.18     1      1.00e+01 1.00e-02 6.34e+01
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 726 "
           pdb=" CB  CYS A 726 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  136.26  -43.26     1      1.00e+01 1.00e-02 2.61e+01
  dihedral pdb=" CB  CYS A 354 "
           pdb=" SG  CYS A 354 "
           pdb=" SG  CYS A 369 "
           pdb=" CB  CYS A 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.23   43.23     1      1.00e+01 1.00e-02 2.61e+01
  ... (remaining 6183 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1136
       0.057 -    0.114: 288
       0.114 -    0.170: 83
       0.170 -    0.227: 13
       0.227 -    0.284: 2
  Chirality restraints: 1522
  Sorted by residual:
  chirality pdb=" CA  PHE B 597 "
            pdb=" N   PHE B 597 "
            pdb=" C   PHE B 597 "
            pdb=" CB  PHE B 597 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CG  LEU A 505 "
            pdb=" CB  LEU A 505 "
            pdb=" CD1 LEU A 505 "
            pdb=" CD2 LEU A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CA  ILE B 300 "
            pdb=" N   ILE B 300 "
            pdb=" C   ILE B 300 "
            pdb=" CB  ILE B 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 1519 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 345 "   -0.080 5.00e-02 4.00e+02   1.21e-01 2.36e+01
        pdb=" N   PRO B 346 "    0.210 5.00e-02 4.00e+02
        pdb=" CA  PRO B 346 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO B 346 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 704 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   ILE B 704 "    0.073 2.00e-02 2.50e+03
        pdb=" O   ILE B 704 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   HIS B 705 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 302 "   -0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C   LEU A 302 "    0.067 2.00e-02 2.50e+03
        pdb=" O   LEU A 302 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LEU A 303 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 146
        2.61 -     3.19: 9153
        3.19 -     3.76: 15228
        3.76 -     4.33: 21364
        4.33 -     4.90: 34076
  Nonbonded interactions: 79967
  Sorted by model distance:
  nonbonded pdb=" N   LYS B 608 "
            pdb=" OE2 GLU B 612 "
     model   vdw
     2.044 3.120
  nonbonded pdb=" O   LYS A 748 "
            pdb=" OG1 THR A 751 "
     model   vdw
     2.124 3.040
  nonbonded pdb=" OD2 ASP B 244 "
            pdb="MN    MN B 801 "
     model   vdw
     2.142 2.320
  nonbonded pdb=" OD2 ASP A 671 "
            pdb=" NH1 ARG A 673 "
     model   vdw
     2.163 3.120
  nonbonded pdb=" OD2 ASP A 244 "
            pdb="MN    MN A 801 "
     model   vdw
     2.166 2.320
  ... (remaining 79962 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:             2.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.880
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5868
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  10426  Z= 0.243
  Angle     :  0.972  10.787  14140  Z= 0.546
  Chirality :  0.057   0.284   1522
  Planarity :  0.007   0.121   1784
  Dihedral  : 14.981  87.902   3822
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 18.99
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.79 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  2.91 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.23), residues: 1210
  helix: -0.67 (0.24), residues: 424
  sheet: -2.03 (0.39), residues: 154
  loop : -0.93 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.056   0.001   ARG A 673 
 TYR   0.038   0.002   TYR A 702 
 PHE   0.036   0.002   PHE A 734 
 TRP   0.062   0.003   TRP B 679 
 HIS   0.011   0.002   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (10422)
  covalent geometry    : angle       0.97143 (14132)
  SS BOND              : bond        0.00115 (    4)
  SS BOND              : angle       1.40007 (    8)
  hydrogen bonds       : bond        0.16656 (  355)
  hydrogen bonds       : angle       6.83782 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 290
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.6789 (m-30) cc_final: 0.6346 (m-30)
REVERT: A  260 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8693 (mmtm)
REVERT: A  261 PHE cc_start: 0.6815 (m-80) cc_final: 0.6063 (m-80)
REVERT: A  377 LYS cc_start: 0.7191 (mptt) cc_final: 0.6978 (mmtm)
REVERT: A  397 PHE cc_start: 0.8386 (m-10) cc_final: 0.8094 (m-10)
REVERT: A  428 GLU cc_start: 0.8156 (pm20) cc_final: 0.7796 (pm20)
REVERT: A  432 LYS cc_start: 0.8413 (ptpp) cc_final: 0.8209 (ptpp)
REVERT: A  493 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7635 (ptpt)
REVERT: A  515 ARG cc_start: 0.7506 (mpp80) cc_final: 0.7204 (mpp80)
REVERT: A  619 MET cc_start: 0.7428 (tmm) cc_final: 0.6811 (tmm)
REVERT: A  691 GLN cc_start: 0.8098 (mm110) cc_final: 0.7877 (mm110)
REVERT: A  734 PHE cc_start: 0.7592 (t80) cc_final: 0.7359 (t80)
REVERT: A  738 MET cc_start: 0.8041 (ttt) cc_final: 0.7707 (ttt)
REVERT: B  179 GLU cc_start: 0.7666 (pt0) cc_final: 0.7187 (pt0)
REVERT: B  223 MET cc_start: 0.7006 (tmm) cc_final: 0.6491 (tmm)
REVERT: B  229 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7613 (tmtt)
REVERT: B  315 MET cc_start: 0.8460 (ptp) cc_final: 0.8085 (ptp)
REVERT: B  407 TYR cc_start: 0.7309 (t80) cc_final: 0.6855 (t80)
REVERT: B  482 MET cc_start: 0.5001 (tpt) cc_final: 0.4676 (tpt)
REVERT: B  489 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7990 (mm-30)
REVERT: B  512 GLN cc_start: 0.8456 (mt0) cc_final: 0.8198 (mt0)
REVERT: B  515 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.7940 (ttp-110)
REVERT: B  531 TYR cc_start: 0.7846 (m-10) cc_final: 0.7479 (m-10)
REVERT: B  547 ARG cc_start: 0.8077 (ptm160) cc_final: 0.7652 (ptm160)
REVERT: B  559 MET cc_start: 0.5376 (ppp) cc_final: 0.4706 (ppp)
REVERT: B  560 PHE cc_start: 0.6032 (t80) cc_final: 0.5761 (t80)
REVERT: B  626 ARG cc_start: 0.6960 (tpp80) cc_final: 0.6579 (tpp80)
REVERT: B  708 HIS cc_start: 0.5965 (t-90) cc_final: 0.5569 (t-90)
  outliers start: 12
  outliers final: 5
  residues processed: 297
  average time/residue: 0.1240
  time to fit residues: 48.9297
Evaluate side-chains
  278 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 273
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 LEU
Chi-restraints excluded: chain B residue  500 SER
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  597 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN
A 532 HIS
A 684 HIS
B 285 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 HIS
B 532 HIS
** B 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.210347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.174185 restraints weight = 17995.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.180061 restraints weight = 10480.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.184242 restraints weight = 7082.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.186853 restraints weight = 5321.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.188796 restraints weight = 4337.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5933
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  10426  Z= 0.135
  Angle     :  0.656  11.206  14140  Z= 0.335
  Chirality :  0.044   0.209   1522
  Planarity :  0.005   0.107   1784
  Dihedral  :  4.964  56.201   1365
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.56 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.24), residues: 1210
  helix:  0.11 (0.25), residues: 442
  sheet: -1.65 (0.40), residues: 150
  loop : -0.59 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 673 
 TYR   0.017   0.002   TYR A 370 
 PHE   0.018   0.001   PHE B 338 
 TRP   0.015   0.001   TRP B 679 
 HIS   0.012   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10422)
  covalent geometry    : angle       0.65569 (14132)
  SS BOND              : bond        0.00052 (    4)
  SS BOND              : angle       0.40920 (    8)
  hydrogen bonds       : bond        0.04479 (  355)
  hydrogen bonds       : angle       5.19816 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 268
  time to evaluate  : 0.299 
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  152 ASP cc_start: 0.6884 (m-30) cc_final: 0.6340 (m-30)
REVERT: A  260 LYS cc_start: 0.9046 (mmtm) cc_final: 0.8677 (mmtm)
REVERT: A  261 PHE cc_start: 0.6917 (m-80) cc_final: 0.5963 (m-80)
REVERT: A  397 PHE cc_start: 0.8269 (m-10) cc_final: 0.7903 (m-10)
REVERT: A  428 GLU cc_start: 0.8193 (pm20) cc_final: 0.7715 (pm20)
REVERT: A  432 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7959 (ptpp)
REVERT: A  450 ARG cc_start: 0.7168 (tmm-80) cc_final: 0.6935 (tmm-80)
REVERT: A  460 PHE cc_start: 0.7172 (t80) cc_final: 0.6773 (m-80)
REVERT: A  472 THR cc_start: 0.6734 (p) cc_final: 0.6532 (t)
REVERT: A  493 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7765 (ptpt)
REVERT: A  515 ARG cc_start: 0.7678 (mpp80) cc_final: 0.7292 (mpp80)
REVERT: A  619 MET cc_start: 0.7665 (tmm) cc_final: 0.7156 (tmm)
REVERT: A  652 GLU cc_start: 0.7859 (mp0) cc_final: 0.7655 (mp0)
REVERT: A  669 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6824 (mt-10)
REVERT: A  691 GLN cc_start: 0.8260 (mm110) cc_final: 0.7967 (mm110)
REVERT: A  736 GLN cc_start: 0.8005 (mp10) cc_final: 0.7792 (mp10)
REVERT: A  738 MET cc_start: 0.8073 (ttt) cc_final: 0.7822 (ttt)
REVERT: B  179 GLU cc_start: 0.7490 (pt0) cc_final: 0.6917 (pt0)
REVERT: B  223 MET cc_start: 0.6759 (tmm) cc_final: 0.6522 (tmm)
REVERT: B  229 LYS cc_start: 0.7975 (tmtt) cc_final: 0.7402 (tmtt)
REVERT: B  489 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7739 (mm-30)
REVERT: B  512 GLN cc_start: 0.8108 (mt0) cc_final: 0.7887 (mt0)
REVERT: B  515 ARG cc_start: 0.8080 (ptp-110) cc_final: 0.7558 (ttp-110)
REVERT: B  536 LYS cc_start: 0.7681 (ttmm) cc_final: 0.7381 (mttm)
REVERT: B  547 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7228 (ptm160)
REVERT: B  559 MET cc_start: 0.5648 (ppp) cc_final: 0.5036 (ppp)
REVERT: B  560 PHE cc_start: 0.6255 (t80) cc_final: 0.6034 (t80)
REVERT: B  626 ARG cc_start: 0.6921 (tpp80) cc_final: 0.6461 (tpp80)
REVERT: B  653 TRP cc_start: 0.7481 (t60) cc_final: 0.7019 (t60)
REVERT: B  708 HIS cc_start: 0.6014 (t-90) cc_final: 0.5614 (t-90)
  outliers start: 15
  outliers final: 9
  residues processed: 275
  average time/residue: 0.1177
  time to fit residues: 42.6560
Evaluate side-chains
  276 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 267
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 532 HIS
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.205385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.169580 restraints weight = 17858.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.175287 restraints weight = 10382.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.179384 restraints weight = 7018.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.181873 restraints weight = 5254.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.183815 restraints weight = 4269.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6055
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10426  Z= 0.159
  Angle     :  0.630  11.958  14140  Z= 0.319
  Chirality :  0.044   0.200   1522
  Planarity :  0.004   0.047   1784
  Dihedral  :  4.751  50.086   1360
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.75 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.24), residues: 1210
  helix:  0.43 (0.25), residues: 436
  sheet: -1.46 (0.40), residues: 150
  loop : -0.56 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 455 
 TYR   0.023   0.002   TYR B 350 
 PHE   0.020   0.002   PHE A 657 
 TRP   0.015   0.001   TRP A 316 
 HIS   0.008   0.001   HIS A 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10422)
  covalent geometry    : angle       0.62960 (14132)
  SS BOND              : bond        0.00095 (    4)
  SS BOND              : angle       0.44578 (    8)
  hydrogen bonds       : bond        0.03916 (  355)
  hydrogen bonds       : angle       4.98891 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 276
  time to evaluate  : 0.365 
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  152 ASP cc_start: 0.7062 (m-30) cc_final: 0.6532 (m-30)
REVERT: A  260 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8750 (mmtm)
REVERT: A  261 PHE cc_start: 0.6943 (m-80) cc_final: 0.5985 (m-80)
REVERT: A  397 PHE cc_start: 0.8316 (m-10) cc_final: 0.7909 (m-10)
REVERT: A  428 GLU cc_start: 0.8183 (pm20) cc_final: 0.7559 (pm20)
REVERT: A  432 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8009 (ptpp)
REVERT: A  450 ARG cc_start: 0.7585 (tmm-80) cc_final: 0.7383 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8260 (ptpt) cc_final: 0.7814 (ptpt)
REVERT: A  515 ARG cc_start: 0.7817 (mpp80) cc_final: 0.7306 (mpp80)
REVERT: A  559 MET cc_start: 0.6871 (ppp) cc_final: 0.6386 (ppp)
REVERT: A  617 LEU cc_start: 0.8447 (mp) cc_final: 0.8234 (mp)
REVERT: A  619 MET cc_start: 0.7793 (tmm) cc_final: 0.7186 (tmm)
REVERT: A  657 PHE cc_start: 0.6169 (t80) cc_final: 0.5725 (t80)
REVERT: A  691 GLN cc_start: 0.8399 (mm110) cc_final: 0.8121 (mm110)
REVERT: A  736 GLN cc_start: 0.8063 (mt0) cc_final: 0.7784 (mp10)
REVERT: B  179 GLU cc_start: 0.7600 (pt0) cc_final: 0.7007 (pt0)
REVERT: B  223 MET cc_start: 0.6705 (tmm) cc_final: 0.6444 (tmm)
REVERT: B  229 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7820 (tmtt)
REVERT: B  245 ILE cc_start: 0.8188 (mm) cc_final: 0.7837 (mm)
REVERT: B  300 ILE cc_start: 0.7759 (mm) cc_final: 0.7556 (mm)
REVERT: B  349 VAL cc_start: 0.6622 (m) cc_final: 0.6131 (p)
REVERT: B  489 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7806 (mm-30)
REVERT: B  509 GLU cc_start: 0.7734 (mt-10) cc_final: 0.6931 (mt-10)
REVERT: B  512 GLN cc_start: 0.8177 (mt0) cc_final: 0.7920 (mt0)
REVERT: B  515 ARG cc_start: 0.8163 (ptp-110) cc_final: 0.7619 (ttp-110)
REVERT: B  559 MET cc_start: 0.5626 (ppp) cc_final: 0.5269 (ppp)
REVERT: B  653 TRP cc_start: 0.7590 (t60) cc_final: 0.6957 (t60)
REVERT: B  708 HIS cc_start: 0.6185 (t-90) cc_final: 0.5791 (t-90)
REVERT: B  740 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7291 (mtm-85)
  outliers start: 20
  outliers final: 15
  residues processed: 287
  average time/residue: 0.1226
  time to fit residues: 46.9305
Evaluate side-chains
  282 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 267
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  456 THR
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 118 optimal weight:    0.3980
   chunk 94 optimal weight:    0.7980
   chunk 101 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 110 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.207614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.169539 restraints weight = 18077.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.175639 restraints weight = 10418.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.179925 restraints weight = 7048.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.182446 restraints weight = 5305.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.184610 restraints weight = 4372.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10426  Z= 0.129
  Angle     :  0.618  12.193  14140  Z= 0.310
  Chirality :  0.043   0.183   1522
  Planarity :  0.004   0.046   1784
  Dihedral  :  4.552  43.560   1360
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.21 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.24), residues: 1210
  helix:  0.55 (0.25), residues: 436
  sheet: -1.37 (0.39), residues: 150
  loop : -0.52 (0.25), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 413 
 TYR   0.026   0.001   TYR B 407 
 PHE   0.019   0.001   PHE A 657 
 TRP   0.016   0.001   TRP B 316 
 HIS   0.008   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10422)
  covalent geometry    : angle       0.61775 (14132)
  SS BOND              : bond        0.00055 (    4)
  SS BOND              : angle       0.35178 (    8)
  hydrogen bonds       : bond        0.03623 (  355)
  hydrogen bonds       : angle       4.77309 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 283
  time to evaluate  : 0.333 
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  152 ASP cc_start: 0.7097 (m-30) cc_final: 0.6604 (m-30)
REVERT: A  260 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8771 (mmtm)
REVERT: A  261 PHE cc_start: 0.6987 (m-80) cc_final: 0.5982 (m-80)
REVERT: A  397 PHE cc_start: 0.8352 (m-10) cc_final: 0.7941 (m-10)
REVERT: A  428 GLU cc_start: 0.8202 (pm20) cc_final: 0.7564 (pm20)
REVERT: A  432 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8023 (ptpp)
REVERT: A  450 ARG cc_start: 0.7612 (tmm-80) cc_final: 0.7386 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8285 (ptpt) cc_final: 0.7865 (ptpt)
REVERT: A  515 ARG cc_start: 0.7894 (mpp80) cc_final: 0.7340 (mpp80)
REVERT: A  559 MET cc_start: 0.6880 (ppp) cc_final: 0.6409 (ppp)
REVERT: A  617 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: A  619 MET cc_start: 0.7816 (tmm) cc_final: 0.7223 (tmm)
REVERT: A  658 GLU cc_start: 0.7789 (pt0) cc_final: 0.7325 (pt0)
REVERT: A  691 GLN cc_start: 0.8331 (mm110) cc_final: 0.8018 (mm-40)
REVERT: A  735 GLN cc_start: 0.8652 (mt0) cc_final: 0.8201 (mt0)
REVERT: B  151 ARG cc_start: 0.7896 (mtp180) cc_final: 0.7023 (ptt-90)
REVERT: B  179 GLU cc_start: 0.7515 (pt0) cc_final: 0.6972 (pt0)
REVERT: B  223 MET cc_start: 0.6657 (tmm) cc_final: 0.6098 (tmm)
REVERT: B  229 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7734 (tmtt)
REVERT: B  245 ILE cc_start: 0.8185 (mm) cc_final: 0.7916 (mm)
REVERT: B  349 VAL cc_start: 0.6737 (m) cc_final: 0.6202 (p)
REVERT: B  357 ASN cc_start: 0.7711 (p0) cc_final: 0.7385 (p0)
REVERT: B  489 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7747 (mm-30)
REVERT: B  509 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6894 (mt-10)
REVERT: B  512 GLN cc_start: 0.8090 (mt0) cc_final: 0.7834 (mt0)
REVERT: B  515 ARG cc_start: 0.8156 (ptp-110) cc_final: 0.7728 (ttm110)
REVERT: B  547 ARG cc_start: 0.8219 (ptp-110) cc_final: 0.7903 (ptm160)
REVERT: B  568 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.7509 (Cg_exo)
REVERT: B  653 TRP cc_start: 0.7587 (t60) cc_final: 0.6867 (t60)
REVERT: B  740 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7233 (mtm-85)
  outliers start: 25
  outliers final: 18
  residues processed: 295
  average time/residue: 0.1252
  time to fit residues: 49.1832
Evaluate side-chains
  293 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 274
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  739 SER
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  594 VAL
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0570
   chunk 103 optimal weight:    0.3980
   chunk 90 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0670
   chunk 31 optimal weight:    0.7980
   chunk 59 optimal weight:    8.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 684 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
B 708 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.209183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.172543 restraints weight = 17926.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.178432 restraints weight = 10636.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.181608 restraints weight = 7293.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.184950 restraints weight = 5756.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.186621 restraints weight = 4637.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6017
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10426  Z= 0.111
  Angle     :  0.601  11.281  14140  Z= 0.301
  Chirality :  0.043   0.240   1522
  Planarity :  0.004   0.058   1784
  Dihedral  :  4.136  21.720   1357
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.85 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.24), residues: 1210
  helix:  0.52 (0.25), residues: 440
  sheet: -1.18 (0.41), residues: 140
  loop : -0.51 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 626 
 TYR   0.017   0.001   TYR B 407 
 PHE   0.012   0.001   PHE A 657 
 TRP   0.016   0.001   TRP B 189 
 HIS   0.009   0.001   HIS B 684 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10422)
  covalent geometry    : angle       0.60133 (14132)
  SS BOND              : bond        0.00045 (    4)
  SS BOND              : angle       0.33655 (    8)
  hydrogen bonds       : bond        0.03390 (  355)
  hydrogen bonds       : angle       4.69229 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 279
  time to evaluate  : 0.382 
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  152 ASP cc_start: 0.7035 (m-30) cc_final: 0.6526 (m-30)
REVERT: A  260 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8845 (mmtm)
REVERT: A  261 PHE cc_start: 0.6941 (m-80) cc_final: 0.5895 (m-80)
REVERT: A  356 TRP cc_start: 0.7706 (m100) cc_final: 0.7441 (m100)
REVERT: A  397 PHE cc_start: 0.8282 (m-10) cc_final: 0.7859 (m-10)
REVERT: A  428 GLU cc_start: 0.8149 (pm20) cc_final: 0.7515 (pm20)
REVERT: A  432 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7958 (ptpp)
REVERT: A  450 ARG cc_start: 0.7571 (tmm-80) cc_final: 0.7356 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8271 (ptpt) cc_final: 0.7852 (ptpt)
REVERT: A  515 ARG cc_start: 0.7902 (mpp80) cc_final: 0.7327 (mpp80)
REVERT: A  559 MET cc_start: 0.6804 (ppp) cc_final: 0.6329 (ppp)
REVERT: A  617 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (mp)
REVERT: A  619 MET cc_start: 0.7837 (tmm) cc_final: 0.7311 (tmm)
REVERT: A  658 GLU cc_start: 0.7750 (pt0) cc_final: 0.7253 (pt0)
REVERT: A  691 GLN cc_start: 0.8279 (mm110) cc_final: 0.7922 (mm-40)
REVERT: A  735 GLN cc_start: 0.8661 (mt0) cc_final: 0.8214 (mt0)
REVERT: B  179 GLU cc_start: 0.7463 (pt0) cc_final: 0.6896 (pt0)
REVERT: B  223 MET cc_start: 0.6583 (tmm) cc_final: 0.5953 (tmm)
REVERT: B  229 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7661 (tmtt)
REVERT: B  245 ILE cc_start: 0.8194 (mm) cc_final: 0.7978 (mm)
REVERT: B  349 VAL cc_start: 0.6610 (m) cc_final: 0.6077 (p)
REVERT: B  357 ASN cc_start: 0.7674 (p0) cc_final: 0.7357 (p0)
REVERT: B  489 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7700 (mm-30)
REVERT: B  509 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6827 (mt-10)
REVERT: B  512 GLN cc_start: 0.8007 (mt0) cc_final: 0.7740 (mt0)
REVERT: B  515 ARG cc_start: 0.8101 (ptp-110) cc_final: 0.7657 (ttm110)
REVERT: B  547 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7950 (ptm160)
REVERT: B  569 MET cc_start: 0.7655 (mtm) cc_final: 0.7234 (mtm)
REVERT: B  653 TRP cc_start: 0.7496 (t60) cc_final: 0.6711 (t60)
REVERT: B  740 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7180 (mtm-85)
  outliers start: 26
  outliers final: 16
  residues processed: 290
  average time/residue: 0.1263
  time to fit residues: 48.8661
Evaluate side-chains
  286 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 269
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  487 MET
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 19 optimal weight:   40.0000
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 74 optimal weight:   10.0000
   chunk 76 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 532 HIS
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.200254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.162993 restraints weight = 17986.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.168765 restraints weight = 10355.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.172696 restraints weight = 6990.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.175502 restraints weight = 5235.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.176998 restraints weight = 4253.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  10426  Z= 0.292
  Angle     :  0.757  14.270  14140  Z= 0.387
  Chirality :  0.049   0.245   1522
  Planarity :  0.005   0.054   1784
  Dihedral  :  4.986  23.645   1356
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.30 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.24), residues: 1210
  helix:  0.19 (0.25), residues: 436
  sheet: -1.53 (0.40), residues: 144
  loop : -0.69 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 626 
 TYR   0.036   0.003   TYR B 350 
 PHE   0.030   0.002   PHE A 460 
 TRP   0.029   0.002   TRP B 189 
 HIS   0.012   0.002   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (10422)
  covalent geometry    : angle       0.75723 (14132)
  SS BOND              : bond        0.00202 (    4)
  SS BOND              : angle       0.55453 (    8)
  hydrogen bonds       : bond        0.04701 (  355)
  hydrogen bonds       : angle       5.16418 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.7140 (m-30) cc_final: 0.6663 (m-30)
REVERT: A  172 LEU cc_start: 0.8238 (mp) cc_final: 0.8005 (mp)
REVERT: A  182 LEU cc_start: 0.8967 (mp) cc_final: 0.8733 (mm)
REVERT: A  261 PHE cc_start: 0.7086 (m-80) cc_final: 0.6072 (m-80)
REVERT: A  397 PHE cc_start: 0.8401 (m-10) cc_final: 0.7903 (m-80)
REVERT: A  428 GLU cc_start: 0.8224 (pm20) cc_final: 0.7774 (pm20)
REVERT: A  432 LYS cc_start: 0.8692 (ptpp) cc_final: 0.8171 (ptpp)
REVERT: A  450 ARG cc_start: 0.7759 (tmm-80) cc_final: 0.7499 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8422 (ptpt) cc_final: 0.8019 (ptpt)
REVERT: A  535 TYR cc_start: 0.7922 (m-10) cc_final: 0.7164 (m-10)
REVERT: A  559 MET cc_start: 0.6877 (ppp) cc_final: 0.6333 (ppp)
REVERT: A  560 PHE cc_start: 0.6935 (t80) cc_final: 0.6607 (t80)
REVERT: A  567 LEU cc_start: 0.8385 (tp) cc_final: 0.8041 (tp)
REVERT: A  617 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8288 (mp)
REVERT: A  619 MET cc_start: 0.7819 (tmm) cc_final: 0.7350 (tmm)
REVERT: A  658 GLU cc_start: 0.7852 (pt0) cc_final: 0.7401 (pt0)
REVERT: A  691 GLN cc_start: 0.8251 (mm110) cc_final: 0.8022 (mm110)
REVERT: A  735 GLN cc_start: 0.8693 (mt0) cc_final: 0.8292 (mt0)
REVERT: B  151 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.7544 (tmm-80)
REVERT: B  179 GLU cc_start: 0.7747 (pt0) cc_final: 0.7070 (pt0)
REVERT: B  223 MET cc_start: 0.6753 (tmm) cc_final: 0.6520 (tmm)
REVERT: B  245 ILE cc_start: 0.8301 (mm) cc_final: 0.8016 (mm)
REVERT: B  381 TRP cc_start: 0.8060 (m100) cc_final: 0.7599 (m-90)
REVERT: B  406 GLU cc_start: 0.7279 (tt0) cc_final: 0.6992 (tt0)
REVERT: B  413 ARG cc_start: 0.7793 (ttm-80) cc_final: 0.7533 (tpp80)
REVERT: B  414 ARG cc_start: 0.8367 (tpm170) cc_final: 0.8114 (tpm170)
REVERT: B  486 GLN cc_start: 0.7898 (pm20) cc_final: 0.7530 (pm20)
REVERT: B  489 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7748 (mm-30)
REVERT: B  512 GLN cc_start: 0.8265 (mt0) cc_final: 0.7989 (mt0)
REVERT: B  515 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.7836 (ttm110)
REVERT: B  612 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7937 (mt-10)
REVERT: B  653 TRP cc_start: 0.8057 (t60) cc_final: 0.7290 (t60)
  outliers start: 30
  outliers final: 16
  residues processed: 297
  average time/residue: 0.1218
  time to fit residues: 48.1772
Evaluate side-chains
  296 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 279
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  500 SER
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain B residue  339 ASN
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  597 PHE
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 118 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 114 optimal weight:    0.4980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0060
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
B 359 GLN
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.204665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.167619 restraints weight = 17620.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.173538 restraints weight = 10117.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.177631 restraints weight = 6809.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.180258 restraints weight = 5084.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.182038 restraints weight = 4143.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10426  Z= 0.130
  Angle     :  0.684  12.759  14140  Z= 0.336
  Chirality :  0.045   0.237   1522
  Planarity :  0.004   0.054   1784
  Dihedral  :  4.496  22.859   1356
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.03 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.24), residues: 1210
  helix:  0.26 (0.25), residues: 442
  sheet: -1.33 (0.39), residues: 148
  loop : -0.50 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 626 
 TYR   0.015   0.001   TYR B 199 
 PHE   0.030   0.001   PHE B 625 
 TRP   0.018   0.001   TRP A 356 
 HIS   0.008   0.001   HIS B 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10422)
  covalent geometry    : angle       0.68393 (14132)
  SS BOND              : bond        0.00168 (    4)
  SS BOND              : angle       0.61678 (    8)
  hydrogen bonds       : bond        0.03680 (  355)
  hydrogen bonds       : angle       4.83926 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 274
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.7049 (m-30) cc_final: 0.6627 (m-30)
REVERT: A  182 LEU cc_start: 0.8910 (mp) cc_final: 0.8691 (mm)
REVERT: A  261 PHE cc_start: 0.6994 (m-80) cc_final: 0.6167 (m-80)
REVERT: A  397 PHE cc_start: 0.8349 (m-10) cc_final: 0.7890 (m-80)
REVERT: A  428 GLU cc_start: 0.8177 (pm20) cc_final: 0.7612 (pm20)
REVERT: A  432 LYS cc_start: 0.8657 (ptpp) cc_final: 0.8152 (ptpp)
REVERT: A  450 ARG cc_start: 0.7707 (tmm-80) cc_final: 0.7486 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8301 (ptpt) cc_final: 0.7876 (ptpt)
REVERT: A  505 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6706 (mp)
REVERT: A  515 ARG cc_start: 0.7966 (mpp80) cc_final: 0.7314 (mpp80)
REVERT: A  535 TYR cc_start: 0.7854 (m-10) cc_final: 0.7051 (m-10)
REVERT: A  559 MET cc_start: 0.6850 (ppp) cc_final: 0.6289 (ppp)
REVERT: A  560 PHE cc_start: 0.6872 (t80) cc_final: 0.6587 (t80)
REVERT: A  566 PHE cc_start: 0.7035 (m-80) cc_final: 0.6791 (m-10)
REVERT: A  567 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7762 (tp)
REVERT: A  617 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (mp)
REVERT: A  619 MET cc_start: 0.7837 (tmm) cc_final: 0.7401 (tmm)
REVERT: A  650 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7171 (tmt170)
REVERT: A  652 GLU cc_start: 0.7965 (mp0) cc_final: 0.6881 (mp0)
REVERT: A  691 GLN cc_start: 0.8207 (mm110) cc_final: 0.7952 (mm110)
REVERT: A  735 GLN cc_start: 0.8682 (mt0) cc_final: 0.8309 (mt0)
REVERT: B  151 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.6807 (ptt90)
REVERT: B  179 GLU cc_start: 0.7650 (pt0) cc_final: 0.7011 (pt0)
REVERT: B  245 ILE cc_start: 0.8212 (mm) cc_final: 0.7954 (mm)
REVERT: B  349 VAL cc_start: 0.6541 (m) cc_final: 0.6025 (p)
REVERT: B  357 ASN cc_start: 0.7858 (p0) cc_final: 0.7533 (p0)
REVERT: B  406 GLU cc_start: 0.7119 (tt0) cc_final: 0.6845 (tt0)
REVERT: B  408 ASP cc_start: 0.7368 (t0) cc_final: 0.6990 (t0)
REVERT: B  414 ARG cc_start: 0.8256 (tpm170) cc_final: 0.7982 (tpm170)
REVERT: B  489 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7731 (mm-30)
REVERT: B  504 TYR cc_start: 0.8016 (t80) cc_final: 0.7577 (t80)
REVERT: B  509 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7542 (mt-10)
REVERT: B  569 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7695 (mtm)
REVERT: B  572 LEU cc_start: 0.8709 (tt) cc_final: 0.8508 (tp)
REVERT: B  612 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: B  654 GLU cc_start: 0.7898 (mp0) cc_final: 0.7646 (mp0)
  outliers start: 28
  outliers final: 19
  residues processed: 286
  average time/residue: 0.1155
  time to fit residues: 44.0489
Evaluate side-chains
  292 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 268
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  166 ASN
Chi-restraints excluded: chain B residue  189 TRP
Chi-restraints excluded: chain B residue  339 ASN
Chi-restraints excluded: chain B residue  487 MET
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  597 PHE
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 114 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 119 optimal weight:    0.3980
   chunk 107 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 109 optimal weight:    0.0370
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.207010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.169553 restraints weight = 17604.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.175462 restraints weight = 10198.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.179669 restraints weight = 6896.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.182177 restraints weight = 5172.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.184203 restraints weight = 4248.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6103
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10426  Z= 0.123
  Angle     :  0.690  14.917  14140  Z= 0.335
  Chirality :  0.044   0.227   1522
  Planarity :  0.004   0.054   1784
  Dihedral  :  4.378  27.852   1356
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.76 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.24), residues: 1210
  helix:  0.30 (0.25), residues: 444
  sheet: -1.20 (0.38), residues: 154
  loop : -0.38 (0.25), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 626 
 TYR   0.014   0.001   TYR B 199 
 PHE   0.030   0.001   PHE B 625 
 TRP   0.017   0.001   TRP B 316 
 HIS   0.011   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10422)
  covalent geometry    : angle       0.69010 (14132)
  SS BOND              : bond        0.00110 (    4)
  SS BOND              : angle       0.58424 (    8)
  hydrogen bonds       : bond        0.03557 (  355)
  hydrogen bonds       : angle       4.83662 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 277
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.7053 (m-30) cc_final: 0.6623 (m-30)
REVERT: A  260 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8771 (mmtm)
REVERT: A  261 PHE cc_start: 0.7006 (m-80) cc_final: 0.5979 (m-80)
REVERT: A  397 PHE cc_start: 0.8357 (m-10) cc_final: 0.7912 (m-80)
REVERT: A  402 LEU cc_start: 0.7769 (mt) cc_final: 0.7503 (mp)
REVERT: A  428 GLU cc_start: 0.8179 (pm20) cc_final: 0.7621 (pm20)
REVERT: A  432 LYS cc_start: 0.8638 (ptpp) cc_final: 0.8182 (ptpp)
REVERT: A  450 ARG cc_start: 0.7713 (tmm-80) cc_final: 0.7508 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8269 (ptpt) cc_final: 0.7842 (ptpt)
REVERT: A  495 TRP cc_start: 0.5243 (OUTLIER) cc_final: 0.4797 (t60)
REVERT: A  515 ARG cc_start: 0.7969 (mpp80) cc_final: 0.7388 (mpp80)
REVERT: A  535 TYR cc_start: 0.7852 (m-10) cc_final: 0.6172 (m-10)
REVERT: A  559 MET cc_start: 0.6808 (ppp) cc_final: 0.6251 (ppp)
REVERT: A  560 PHE cc_start: 0.6850 (t80) cc_final: 0.6544 (t80)
REVERT: A  617 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8284 (mp)
REVERT: A  619 MET cc_start: 0.7860 (tmm) cc_final: 0.7420 (tmm)
REVERT: A  650 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7218 (tmt170)
REVERT: A  652 GLU cc_start: 0.7937 (mp0) cc_final: 0.7017 (mp0)
REVERT: A  691 GLN cc_start: 0.8266 (mm110) cc_final: 0.7948 (mm110)
REVERT: A  735 GLN cc_start: 0.8680 (mt0) cc_final: 0.8329 (mt0)
REVERT: B  151 ARG cc_start: 0.8678 (ttp-110) cc_final: 0.6665 (ptt90)
REVERT: B  179 GLU cc_start: 0.7594 (pt0) cc_final: 0.6955 (pt0)
REVERT: B  349 VAL cc_start: 0.6550 (m) cc_final: 0.6064 (p)
REVERT: B  357 ASN cc_start: 0.7670 (p0) cc_final: 0.7289 (p0)
REVERT: B  408 ASP cc_start: 0.7311 (t0) cc_final: 0.6935 (t0)
REVERT: B  489 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: B  504 TYR cc_start: 0.7982 (t80) cc_final: 0.7542 (t80)
REVERT: B  515 ARG cc_start: 0.8124 (ptp-110) cc_final: 0.7699 (ttm110)
REVERT: B  534 VAL cc_start: 0.8032 (m) cc_final: 0.7612 (p)
REVERT: B  612 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7989 (mt-10)
  outliers start: 24
  outliers final: 16
  residues processed: 289
  average time/residue: 0.1128
  time to fit residues: 43.5682
Evaluate side-chains
  290 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 271
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  495 TRP
Chi-restraints excluded: chain A residue  574 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  189 TRP
Chi-restraints excluded: chain B residue  487 MET
Chi-restraints excluded: chain B residue  637 THR
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 19 optimal weight:   50.0000
   chunk 7 optimal weight:    7.9990
   chunk 51 optimal weight:    0.1980
   chunk 81 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 100 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN
** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.205455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.168450 restraints weight = 17511.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.174213 restraints weight = 10094.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.178347 restraints weight = 6826.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.180957 restraints weight = 5103.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.183095 restraints weight = 4163.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
moved from start:          0.4014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10426  Z= 0.152
  Angle     :  0.739  16.627  14140  Z= 0.359
  Chirality :  0.046   0.306   1522
  Planarity :  0.004   0.049   1784
  Dihedral  :  4.511  34.960   1356
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.04 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.46 (0.24), residues: 1210
  helix:  0.27 (0.25), residues: 444
  sheet: -1.18 (0.37), residues: 168
  loop : -0.35 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 626 
 TYR   0.018   0.002   TYR B 350 
 PHE   0.028   0.001   PHE A 657 
 TRP   0.025   0.001   TRP A 356 
 HIS   0.011   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10422)
  covalent geometry    : angle       0.73889 (14132)
  SS BOND              : bond        0.00125 (    4)
  SS BOND              : angle       0.57618 (    8)
  hydrogen bonds       : bond        0.03644 (  355)
  hydrogen bonds       : angle       4.90309 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 279
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.7084 (m-30) cc_final: 0.6656 (m-30)
REVERT: A  260 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8792 (mmtm)
REVERT: A  261 PHE cc_start: 0.7027 (m-80) cc_final: 0.6231 (m-80)
REVERT: A  397 PHE cc_start: 0.8344 (m-10) cc_final: 0.7858 (m-80)
REVERT: A  399 ASN cc_start: 0.7953 (m-40) cc_final: 0.7598 (m-40)
REVERT: A  428 GLU cc_start: 0.8178 (pm20) cc_final: 0.7637 (pm20)
REVERT: A  432 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8091 (ptpp)
REVERT: A  450 ARG cc_start: 0.7752 (tmm-80) cc_final: 0.7477 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7847 (ptpt)
REVERT: A  495 TRP cc_start: 0.5327 (OUTLIER) cc_final: 0.4798 (t60)
REVERT: A  515 ARG cc_start: 0.7962 (mpp80) cc_final: 0.7364 (mpp80)
REVERT: A  535 TYR cc_start: 0.7864 (m-10) cc_final: 0.7176 (m-10)
REVERT: A  559 MET cc_start: 0.6806 (ppp) cc_final: 0.6251 (ppp)
REVERT: A  560 PHE cc_start: 0.6885 (t80) cc_final: 0.6588 (t80)
REVERT: A  617 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8297 (mp)
REVERT: A  619 MET cc_start: 0.7864 (tmm) cc_final: 0.7445 (tmm)
REVERT: A  650 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7181 (tmt170)
REVERT: A  652 GLU cc_start: 0.7905 (mp0) cc_final: 0.7045 (mp0)
REVERT: A  658 GLU cc_start: 0.7732 (pt0) cc_final: 0.7267 (pt0)
REVERT: A  673 ARG cc_start: 0.6507 (ttp-110) cc_final: 0.4854 (ttp80)
REVERT: A  691 GLN cc_start: 0.8253 (mm110) cc_final: 0.7948 (mm110)
REVERT: A  735 GLN cc_start: 0.8670 (mt0) cc_final: 0.8341 (mt0)
REVERT: B  179 GLU cc_start: 0.7668 (pt0) cc_final: 0.7042 (pt0)
REVERT: B  349 VAL cc_start: 0.6671 (m) cc_final: 0.6166 (p)
REVERT: B  357 ASN cc_start: 0.7656 (p0) cc_final: 0.7239 (p0)
REVERT: B  358 VAL cc_start: 0.7692 (t) cc_final: 0.7467 (m)
REVERT: B  381 TRP cc_start: 0.7970 (m100) cc_final: 0.7619 (m-90)
REVERT: B  408 ASP cc_start: 0.7326 (t0) cc_final: 0.6964 (t0)
REVERT: B  489 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: B  504 TYR cc_start: 0.8026 (t80) cc_final: 0.7540 (t80)
REVERT: B  515 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7720 (ttm110)
REVERT: B  534 VAL cc_start: 0.8063 (m) cc_final: 0.7630 (p)
REVERT: B  612 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7951 (mt-10)
  outliers start: 27
  outliers final: 19
  residues processed: 291
  average time/residue: 0.1152
  time to fit residues: 45.1609
Evaluate side-chains
  302 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 280
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  495 TRP
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  189 TRP
Chi-restraints excluded: chain B residue  339 ASN
Chi-restraints excluded: chain B residue  487 MET
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  597 PHE
Chi-restraints excluded: chain B residue  637 THR
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Chi-restraints excluded: chain B residue  738 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 14 optimal weight:   50.0000
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:   20.0000
   chunk 111 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 339 ASN
B 735 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.205033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.167590 restraints weight = 17270.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.173484 restraints weight = 10013.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.177558 restraints weight = 6778.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.180120 restraints weight = 5097.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.181958 restraints weight = 4164.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.4311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6142
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10426  Z= 0.153
  Angle     :  0.760  14.475  14140  Z= 0.369
  Chirality :  0.047   0.347   1522
  Planarity :  0.004   0.049   1784
  Dihedral  :  4.558  33.665   1356
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.40 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.46 (0.24), residues: 1210
  helix:  0.26 (0.25), residues: 444
  sheet: -1.15 (0.39), residues: 158
  loop : -0.37 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 740 
 TYR   0.057   0.002   TYR B 693 
 PHE   0.030   0.002   PHE A 657 
 TRP   0.020   0.001   TRP B 316 
 HIS   0.009   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10422)
  covalent geometry    : angle       0.75985 (14132)
  SS BOND              : bond        0.00139 (    4)
  SS BOND              : angle       0.58301 (    8)
  hydrogen bonds       : bond        0.03642 (  355)
  hydrogen bonds       : angle       4.87203 (  978)

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

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

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2420 Ramachandran restraints generated.
    1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 282
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASP cc_start: 0.7068 (m-30) cc_final: 0.6646 (m-30)
REVERT: A  260 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8815 (mmtm)
REVERT: A  261 PHE cc_start: 0.6918 (m-80) cc_final: 0.6087 (m-80)
REVERT: A  397 PHE cc_start: 0.8361 (m-10) cc_final: 0.7859 (m-80)
REVERT: A  399 ASN cc_start: 0.7963 (m-40) cc_final: 0.7550 (m-40)
REVERT: A  428 GLU cc_start: 0.8188 (pm20) cc_final: 0.7510 (pm20)
REVERT: A  432 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8038 (ptpp)
REVERT: A  450 ARG cc_start: 0.7760 (tmm-80) cc_final: 0.7545 (ttp-170)
REVERT: A  493 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7844 (ptpt)
REVERT: A  495 TRP cc_start: 0.5311 (OUTLIER) cc_final: 0.4744 (t60)
REVERT: A  515 ARG cc_start: 0.7972 (mpp80) cc_final: 0.7394 (mpp80)
REVERT: A  535 TYR cc_start: 0.7797 (m-10) cc_final: 0.5698 (m-10)
REVERT: A  559 MET cc_start: 0.6789 (ppp) cc_final: 0.6215 (ppp)
REVERT: A  560 PHE cc_start: 0.6869 (t80) cc_final: 0.6599 (t80)
REVERT: A  608 LYS cc_start: 0.7745 (mttt) cc_final: 0.7526 (ttmm)
REVERT: A  617 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8294 (mp)
REVERT: A  619 MET cc_start: 0.7878 (tmm) cc_final: 0.7451 (tmm)
REVERT: A  650 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7206 (tmt170)
REVERT: A  652 GLU cc_start: 0.7967 (mp0) cc_final: 0.7230 (mp0)
REVERT: A  673 ARG cc_start: 0.6526 (ttp-110) cc_final: 0.4877 (ttp80)
REVERT: A  691 GLN cc_start: 0.8229 (mm110) cc_final: 0.7962 (mm110)
REVERT: A  735 GLN cc_start: 0.8673 (mt0) cc_final: 0.8357 (mt0)
REVERT: B  151 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8038 (ttm110)
REVERT: B  179 GLU cc_start: 0.7669 (pt0) cc_final: 0.7050 (pt0)
REVERT: B  311 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8201 (tmmt)
REVERT: B  349 VAL cc_start: 0.6669 (m) cc_final: 0.6174 (p)
REVERT: B  357 ASN cc_start: 0.7758 (p0) cc_final: 0.7424 (p0)
REVERT: B  358 VAL cc_start: 0.7663 (t) cc_final: 0.7462 (m)
REVERT: B  381 TRP cc_start: 0.7949 (m100) cc_final: 0.7622 (m-90)
REVERT: B  408 ASP cc_start: 0.7310 (t0) cc_final: 0.6961 (t0)
REVERT: B  489 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7718 (mm-30)
REVERT: B  504 TYR cc_start: 0.7970 (t80) cc_final: 0.7529 (t80)
REVERT: B  515 ARG cc_start: 0.8198 (ptp-110) cc_final: 0.7772 (ttm110)
REVERT: B  534 VAL cc_start: 0.8061 (m) cc_final: 0.7611 (p)
REVERT: B  547 ARG cc_start: 0.8438 (ptp-170) cc_final: 0.8171 (ptp90)
REVERT: B  612 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: B  626 ARG cc_start: 0.7155 (ttm-80) cc_final: 0.6889 (ttm-80)
  outliers start: 25
  outliers final: 18
  residues processed: 293
  average time/residue: 0.1156
  time to fit residues: 45.0249
Evaluate side-chains
  300 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 279
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  495 TRP
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  650 ARG
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain B residue  154 VAL
Chi-restraints excluded: chain B residue  189 TRP
Chi-restraints excluded: chain B residue  339 ASN
Chi-restraints excluded: chain B residue  487 MET
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  554 ILE
Chi-restraints excluded: chain B residue  637 THR
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain B residue  669 GLU
Chi-restraints excluded: chain B residue  687 GLU
Chi-restraints excluded: chain B residue  689 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.0770
   chunk 40 optimal weight:    0.2980
   chunk 14 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.8742

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.204443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.166828 restraints weight = 17414.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.172647 restraints weight = 10041.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.176654 restraints weight = 6790.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.179516 restraints weight = 5085.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.181190 restraints weight = 4143.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6143
moved from start:          0.4275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10426  Z= 0.153
  Angle     :  0.772  14.527  14140  Z= 0.376
  Chirality :  0.046   0.329   1522
  Planarity :  0.004   0.048   1784
  Dihedral  :  4.549  33.338   1356
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 21.31 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.53 (0.24), residues: 1210
  helix:  0.17 (0.24), residues: 446
  sheet: -1.12 (0.38), residues: 168
  loop : -0.39 (0.26), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 626 
 TYR   0.018   0.001   TYR B 350 
 PHE   0.028   0.001   PHE A 657 
 TRP   0.029   0.002   TRP A 356 
 HIS   0.009   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10422)
  covalent geometry    : angle       0.77256 (14132)
  SS BOND              : bond        0.00142 (    4)
  SS BOND              : angle       0.57764 (    8)
  hydrogen bonds       : bond        0.03736 (  355)
  hydrogen bonds       : angle       4.91477 (  978)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2015.44 seconds
wall clock time: 35 minutes 31.09 seconds (2131.09 seconds total)