Starting phenix.real_space_refine
on Thu Mar  5 10:32:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qx3_4661/03_2026/6qx3_4661.map"
  }
  resolution = 3.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     P      14      5.49       5
     S      79      5.16       5
     C    6857      2.51       5
     N    1884      2.21       5
     O    2107      1.98       5
     H   10646      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 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: 21587
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "D"
      Number of atoms: 329
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 329
          Classifications: {'RNA': 10}
          Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 4, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 6}
    Chain: "G"
      Number of atoms: 122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 122
          Classifications: {'RNA': 4}
          Modifications used: {'3*END': 1, 'rna2p_pyr': 4}
          Link IDs: {'rna2p': 3}
    Chain: "O"
      Number of atoms: 1799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1799
          Classifications: {'peptide': 121}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 115}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 9750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 615, 9750
          Classifications: {'peptide': 615}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 28, 'TRANS': 586}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 8157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 515, 8157
          Classifications: {'peptide': 515}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 487}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "C"
      Number of atoms: 1430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 1430
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 6, 'TRANS': 79}
  Time building chain proxies: 3.90, per 1000 atoms: 0.18
  Number of scatterers: 21587
  At special positions: 0
  Unit cell: (103.68, 102.6, 120.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      79     16.00
     P      14     15.00
     O    2107      8.00
     N    1884      7.00
     C    6857      6.00
     H   10646      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.88
  Conformation dependent library (CDL) restraints added in 609.8 milliseconds
  

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2504

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      41.4% alpha, 9.3% beta
      0 base pairs and 5 stacking pairs defined.
    Time for finding SS restraints: 3.74
  Creating SS restraints...
    Processing helix  chain 'O' and resid 28 through 32
      removed outlier: 4.004A  pdb=" N   TYR O  32 " --> pdb=" O   PHE O  29 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 62 through 65
      removed outlier: 4.219A  pdb=" N   LYS O  65 " --> pdb=" O   ASP O  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 62 through 65'
    Processing helix  chain 'O' and resid 87 through 91
      removed outlier: 3.501A  pdb=" N   ASP O  90 " --> pdb=" O   LYS O  87 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER O  91 " --> pdb=" O   PRO O  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 87 through 91'
    Processing helix  chain 'B' and resid 4 through 11
      removed outlier: 3.540A  pdb=" N   LEU B   7 " --> pdb=" O   ASN B   4 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE B   9 " --> pdb=" O   THR B   6 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 3.575A  pdb=" N   VAL B  43 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN B  44 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   HIS B  47 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   TYR B  49 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 99
      removed outlier: 3.698A  pdb=" N   LEU B  89 " --> pdb=" O   THR B  85 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLU B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B  96 " --> pdb=" O   MET B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.866A  pdb=" N   LEU B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU B 109 " --> pdb=" O   ASN B 105 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   VAL B 113 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 124
      removed outlier: 3.954A  pdb=" N   THR B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   GLN B 124 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 119 through 124'
    Processing helix  chain 'B' and resid 140 through 153
      removed outlier: 3.965A  pdb=" N   ALA B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ASN B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
      removed outlier: 3.516A  pdb=" N   GLU B 159 " --> pdb=" O   THR B 156 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   SER B 160 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 174
      removed outlier: 3.518A  pdb=" N   PHE B 166 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP B 169 " --> pdb=" O   ASP B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 4.332A  pdb=" N   ILE B 219 " --> pdb=" O   ARG B 215 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 263
      removed outlier: 4.345A  pdb=" N   PHE B 251 " --> pdb=" O   GLN B 247 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   TYR B 253 " --> pdb=" O   ARG B 249 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B 254 " --> pdb=" O   GLY B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 289
      removed outlier: 3.804A  pdb=" N   LYS B 279 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ALA B 280 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ALA B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   VAL B 285 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL B 286 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.884A  pdb=" N   ASN B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLN B 313 " --> pdb=" O   TRP B 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 308 through 313'
    Processing helix  chain 'B' and resid 314 through 326
      removed outlier: 3.909A  pdb=" N   PHE B 318 " --> pdb=" O   ASN B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 345
      removed outlier: 3.959A  pdb=" N   LEU B 337 " --> pdb=" O   PHE B 333 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   SER B 338 " --> pdb=" O   ARG B 334 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ALA B 340 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 370 through 375
    Processing helix  chain 'B' and resid 382 through 393
      removed outlier: 3.941A  pdb=" N   LYS B 391 " --> pdb=" O   LYS B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 426
      removed outlier: 3.967A  pdb=" N   VAL B 418 " --> pdb=" O   MET B 414 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU B 419 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY B 420 " --> pdb=" O   SER B 416 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ILE B 423 " --> pdb=" O   LEU B 419 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU B 424 " --> pdb=" O   GLY B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 470
      removed outlier: 3.614A  pdb=" N   PHE B 466 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG B 468 " --> pdb=" O   ASP B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 536
      removed outlier: 3.650A  pdb=" N   SER B 524 " --> pdb=" O   SER B 520 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 527 " --> pdb=" O   MET B 523 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR B 528 " --> pdb=" O   SER B 524 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE B 530 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   LYS B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 560
      removed outlier: 3.554A  pdb=" N   ILE B 552 " --> pdb=" O   LEU B 548 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR B 558 " --> pdb=" O   ASP B 554 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 583
      removed outlier: 3.921A  pdb=" N   LEU B 576 " --> pdb=" O   ARG B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 594
      removed outlier: 4.062A  pdb=" N   GLY B 594 " --> pdb=" O   VAL B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 617 through 625
      removed outlier: 3.901A  pdb=" N   CYS B 625 " --> pdb=" O   GLN B 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.581A  pdb=" N   ALA A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR A 232 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
      removed outlier: 3.738A  pdb=" N   SER A 247 " --> pdb=" O   GLU A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
      removed outlier: 3.553A  pdb=" N   CYS A 310 " --> pdb=" O   ASP A 306 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG A 312 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.775A  pdb=" N   LEU A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   SER A 337 " --> pdb=" O   ASN A 333 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 340 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASN A 350 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
      removed outlier: 4.234A  pdb=" N   ALA A 369 " --> pdb=" O   GLN A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 385
    Processing helix  chain 'A' and resid 407 through 412
    Processing helix  chain 'A' and resid 433 through 451
      removed outlier: 3.538A  pdb=" N   TYR A 437 " --> pdb=" O   ALA A 433 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A 439 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 460
      removed outlier: 3.982A  pdb=" N   TYR A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 476
      removed outlier: 4.204A  pdb=" N   TYR A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE A 465 " --> pdb=" O   LYS A 461 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ASN A 466 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   CYS A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A 475 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 600
      removed outlier: 4.120A  pdb=" N   LEU A 586 " --> pdb=" O   ARG A 582 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLN A 591 " --> pdb=" O   GLN A 587 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ILE A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   GLU A 599 " --> pdb=" O   MET A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
      removed outlier: 3.516A  pdb=" N   PHE A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   PHE A 612 " --> pdb=" O   THR A 608 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 607 through 612'
    Processing helix  chain 'A' and resid 632 through 650
      removed outlier: 4.487A  pdb=" N   LEU A 641 " --> pdb=" O   CYS A 637 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER A 648 " --> pdb=" O   SER A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 662
      removed outlier: 3.803A  pdb=" N   GLU A 656 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 660 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 674
      removed outlier: 3.535A  pdb=" N   LEU A 672 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 692
      removed outlier: 3.648A  pdb=" N   ALA A 689 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 711
      removed outlier: 4.352A  pdb=" N   SER A 705 " --> pdb=" O   LEU A 701 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ASN A 708 " --> pdb=" O   ALA A 704 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A 709 " --> pdb=" O   SER A 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 53
      removed outlier: 4.235A  pdb=" N   ARG C  46 " --> pdb=" O   ASN C  42 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   MET C  51 " --> pdb=" O   MET C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 67
      removed outlier: 4.166A  pdb=" N   GLU C  65 " --> pdb=" O   LYS C  61 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   MET C  66 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 61 through 67'
    Processing helix  chain 'C' and resid 93 through 102
      removed outlier: 3.676A  pdb=" N   THR C  97 " --> pdb=" O   PRO C  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 115
      removed outlier: 3.620A  pdb=" N   TYR C 115 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 126
      removed outlier: 3.715A  pdb=" N   LYS C 121 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   VAL C 122 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU C 123 " --> pdb=" O   PHE C 119 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG C 124 " --> pdb=" O   GLU C 120 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS C 126 " --> pdb=" O   VAL C 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 3 through 7
      removed outlier: 3.861A  pdb=" N   GLN O   3 " --> pdb=" O   SER O  25 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER O  25 " --> pdb=" O   GLN O   3 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU O  23 " --> pdb=" O   GLN O   5 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER O  21 " --> pdb=" O   SER O   7 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU O  81 " --> pdb=" O   LEU O  20 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   CYS O  22 " --> pdb=" O   LEU O  79 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU O  79 " --> pdb=" O   CYS O  22 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ASP O  73 " --> pdb=" O   THR O  78 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   SER O  71 " --> pdb=" O   TYR O  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 58 through 60
      removed outlier: 3.986A  pdb=" N   THR O  59 " --> pdb=" O   MET O  50 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   MET O  50 " --> pdb=" O   THR O  59 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TRP O  36 " --> pdb=" O   VAL O  48 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   MET O  50 " --> pdb=" O   MET O  34 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   MET O  34 " --> pdb=" O   MET O  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 57
      removed outlier: 3.580A  pdb=" N   THR B  56 " --> pdb=" O   GLN B  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 130
      removed outlier: 3.677A  pdb=" N   ASP B 130 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ARG B 135 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 227
      removed outlier: 3.520A  pdb=" N   ILE B 241 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 437 through 442
      removed outlier: 3.520A  pdb=" N   TRP B 437 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASP B 439 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE B 447 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLY B 304 " --> pdb=" O   PHE B 447 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 449 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 483 " --> pdb=" O   THR B 303 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 350
      removed outlier: 3.741A  pdb=" N   ALA B 401 " --> pdb=" O   ALA B 349 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 359
      removed outlier: 3.555A  pdb=" N   LEU B 364 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLN B 367 " --> pdb=" O   VAL A 379 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 317 through 324
      removed outlier: 6.081A  pdb=" N   ILE A 545 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   LEU A 543 " --> pdb=" O   PRO A 320 " (cutoff:3.500A)
      removed outlier: 9.113A  pdb=" N   ILE A 322 " --> pdb=" O   CYS A 541 " (cutoff:3.500A)
      removed outlier: 11.117A  pdb=" N   CYS A 541 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 563 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   MET A 561 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLU A 524 " --> pdb=" O   TYR A 564 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 525 " --> pdb=" O   TYR A 501 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   TYR A 501 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
      removed outlier: 5.801A  pdb=" N   THR A 498 " --> pdb=" O   CYS A 489 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   CYS A 489 " --> pdb=" O   THR A 498 " (cutoff:3.500A)
      removed outlier: 5.016A  pdb=" N   LEU A 500 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   SER A 487 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLY A 502 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 57 through 58
      removed outlier: 3.870A  pdb=" N   ILE C  57 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL C  91 " --> pdb=" O   ILE C  57 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   MET C  90 " --> pdb=" O   SER C  79 " (cutoff:3.500A)

    305 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      5 stacking parallelities
  Total time for adding SS restraints: 4.98

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10625
        1.03 -     1.23: 39
        1.23 -     1.42: 4686
        1.42 -     1.62: 6363
        1.62 -     1.81: 137
  Bond restraints: 21850
  Sorted by residual:
  bond pdb=" C   ASN A 331 "
       pdb=" N   PRO A 332 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.08e-02 8.57e+03 3.16e+00
  bond pdb=" CB  VAL A 636 "
       pdb=" CG2 VAL A 636 "
    ideal  model  delta    sigma   weight residual
    1.521  1.475  0.046 3.30e-02 9.18e+02 1.93e+00
  bond pdb=" CB  PRO B  29 "
       pdb=" CG  PRO B  29 "
    ideal  model  delta    sigma   weight residual
    1.492  1.425  0.067 5.00e-02 4.00e+02 1.81e+00
  bond pdb=" C   ILE B 667 "
       pdb=" N   PRO B 668 "
    ideal  model  delta    sigma   weight residual
    1.330  1.347 -0.017 1.25e-02 6.40e+03 1.79e+00
  bond pdb=" CB  LYS B 471 "
       pdb=" CG  LYS B 471 "
    ideal  model  delta    sigma   weight residual
    1.520  1.482  0.038 3.00e-02 1.11e+03 1.61e+00
  ... (remaining 21845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 38666
        2.01 -     4.02: 687
        4.02 -     6.03: 72
        6.03 -     8.04: 3
        8.04 -    10.05: 1
  Bond angle restraints: 39429
  Sorted by residual:
  angle pdb=" C1'   C G  11 "
        pdb=" N1    C G  11 "
        pdb=" C2    C G  11 "
      ideal   model   delta    sigma   weight residual
     118.80  128.85  -10.05 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C   PRO B  28 "
        pdb=" N   PRO B  29 "
        pdb=" CA  PRO B  29 "
      ideal   model   delta    sigma   weight residual
     119.84  115.83    4.01 1.25e+00 6.40e-01 1.03e+01
  angle pdb=" N   GLY B 564 "
        pdb=" CA  GLY B 564 "
        pdb=" C   GLY B 564 "
      ideal   model   delta    sigma   weight residual
     112.50  116.15   -3.65 1.16e+00 7.43e-01 9.89e+00
  angle pdb=" N   GLU A 613 "
        pdb=" CA  GLU A 613 "
        pdb=" C   GLU A 613 "
      ideal   model   delta    sigma   weight residual
     110.91  107.30    3.61 1.17e+00 7.31e-01 9.50e+00
  angle pdb=" CA  PRO B  28 "
        pdb=" C   PRO B  28 "
        pdb=" N   PRO B  29 "
      ideal   model   delta    sigma   weight residual
     117.93  121.60   -3.67 1.20e+00 6.94e-01 9.35e+00
  ... (remaining 39424 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.10: 9683
       26.10 -    52.21: 520
       52.21 -    78.31: 96
       78.31 -   104.42: 11
      104.42 -   130.52: 1
  Dihedral angle restraints: 10311
    sinusoidal: 5763
      harmonic: 4548
  Sorted by residual:
  dihedral pdb=" O4'   C G  11 "
           pdb=" C1'   C G  11 "
           pdb=" N1    C G  11 "
           pdb=" C2    C G  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00  101.48  130.52     1      1.70e+01 3.46e-03 5.48e+01
  dihedral pdb=" O4'   U G   9 "
           pdb=" C1'   U G   9 "
           pdb=" N1    U G   9 "
           pdb=" C2    U G   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -49.85  -78.15     1      1.70e+01 3.46e-03 2.64e+01
  dihedral pdb=" CA  GLN B 442 "
           pdb=" C   GLN B 442 "
           pdb=" N   SER B 443 "
           pdb=" CA  SER B 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 10308 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 927
       0.032 -    0.063: 526
       0.063 -    0.095: 148
       0.095 -    0.127: 55
       0.127 -    0.158: 10
  Chirality restraints: 1666
  Sorted by residual:
  chirality pdb=" C1'   C G  11 "
            pdb=" O4'   C G  11 "
            pdb=" C2'   C G  11 "
            pdb=" N1    C G  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.29    0.16 2.00e-01 2.50e+01 6.26e-01
  chirality pdb=" CA  ILE B 606 "
            pdb=" N   ILE B 606 "
            pdb=" C   ILE B 606 "
            pdb=" CB  ILE B 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  ILE B 475 "
            pdb=" N   ILE B 475 "
            pdb=" C   ILE B 475 "
            pdb=" CB  ILE B 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1663 not shown)

  Planarity restraints: 3190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B  28 "    0.044 5.00e-02 4.00e+02   6.49e-02 6.75e+00
        pdb=" N   PRO B  29 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B  29 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  29 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B  23 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.21e+00
        pdb=" C   PRO B  23 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   PRO B  23 "    0.013 2.00e-02 2.50e+03
        pdb=" N   TYR B  24 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 219 "   -0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO A 220 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 3187 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 3598
        2.27 -     2.85: 47581
        2.85 -     3.44: 50761
        3.44 -     4.02: 69994
        4.02 -     4.60: 109075
  Nonbonded interactions: 281009
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP O  90 "
            pdb=" HH  TYR O  94 "
     model   vdw
     1.690 2.450
  nonbonded pdb=" HE  ARG A 566 "
            pdb=" O   THR A 567 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" HZ1 LYS B 347 "
            pdb=" O   GLY B 406 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" HZ1 LYS B 168 "
            pdb=" O   GLU A 203 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" OD1 ASN B 455 "
            pdb=" H   GLY B 458 "
     model   vdw
     1.726 2.450
  ... (remaining 281004 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:             0.120
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     24.110
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
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      :  0.007   0.067  11204  Z= 0.265
  Angle     :  0.772  10.055  15209  Z= 0.411
  Chirality :  0.043   0.158   1666
  Planarity :  0.004   0.065   1914
  Dihedral  : 15.059 130.521   4299
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  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: -5.16 (0.18), residues: 1325
  helix: -4.00 (0.13), residues: 459
  sheet: -3.57 (0.37), residues: 130
  loop : -3.05 (0.21), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 663 
 TYR   0.015   0.002   TYR B  24 
 PHE   0.021   0.002   PHE A 520 
 TRP   0.021   0.002   TRP B 580 
 HIS   0.006   0.002   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 (11204)
  covalent geometry    : angle       0.77222 (15209)
  hydrogen bonds       : bond        0.32656 (  305)
  hydrogen bonds       : angle       9.89871 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  251 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 GLN cc_start: 0.7644 (pt0) cc_final: 0.7231 (pp30)
REVERT: B  220 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7872 (ttm-80)
REVERT: B  290 MET cc_start: 0.7411 (tpt) cc_final: 0.7067 (ppp)
REVERT: B  342 ILE cc_start: 0.8763 (mm) cc_final: 0.8459 (mt)
REVERT: B  357 PHE cc_start: 0.7429 (m-80) cc_final: 0.6978 (m-80)
REVERT: B  358 GLU cc_start: 0.8110 (pp20) cc_final: 0.7653 (pp20)
REVERT: B  476 ASN cc_start: 0.8096 (m-40) cc_final: 0.7889 (m-40)
REVERT: B  531 LYS cc_start: 0.7794 (ttpt) cc_final: 0.6926 (tptt)
REVERT: A  716 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.7261 (mtt90)
REVERT: C   53 MET cc_start: 0.7525 (tpp) cc_final: 0.7317 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.3208
  time to fit residues: 105.9757
Evaluate side-chains
  179 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0470
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.7884

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

Flipped N/Q/H residues before XYZ refinement:
B 621 GLN
A 466 ASN
A 591 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.177167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148897 restraints weight = 43427.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.153309 restraints weight = 23378.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.156117 restraints weight = 15986.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157756 restraints weight = 12756.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.158415 restraints weight = 11151.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11204  Z= 0.122
  Angle     :  0.570   6.565  15209  Z= 0.302
  Chirality :  0.038   0.142   1666
  Planarity :  0.005   0.055   1914
  Dihedral  : 10.500 127.675   1654
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  8.65 %
    Favored  : 90.83 %
  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: -4.03 (0.20), residues: 1325
  helix: -2.40 (0.19), residues: 483
  sheet: -3.10 (0.36), residues: 143
  loop : -2.81 (0.22), residues: 699

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 249 
 TYR   0.020   0.001   TYR B  24 
 PHE   0.012   0.001   PHE B 318 
 TRP   0.014   0.001   TRP B 580 
 HIS   0.005   0.001   HIS B 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11204)
  covalent geometry    : angle       0.56993 (15209)
  hydrogen bonds       : bond        0.05447 (  305)
  hydrogen bonds       : angle       5.67496 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  198 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 192
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   90 ASP cc_start: 0.7758 (t0) cc_final: 0.7512 (t0)
REVERT: B   65 GLN cc_start: 0.7647 (pt0) cc_final: 0.7161 (pp30)
REVERT: B  124 GLN cc_start: 0.8187 (pp30) cc_final: 0.7722 (pt0)
REVERT: B  148 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7576 (tm-30)
REVERT: B  342 ILE cc_start: 0.8983 (mm) cc_final: 0.8749 (mt)
REVERT: B  356 MET cc_start: 0.7243 (mmt) cc_final: 0.6214 (mmm)
REVERT: B  554 ASP cc_start: 0.8231 (m-30) cc_final: 0.7339 (t0)
REVERT: A  460 MET cc_start: 0.7479 (mmt) cc_final: 0.7266 (mmt)
REVERT: A  501 TYR cc_start: 0.8293 (m-80) cc_final: 0.7958 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 195
  average time/residue: 0.2933
  time to fit residues: 77.8700
Evaluate side-chains
  170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 165
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain C residue   97 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
C  42 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.171680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.141379 restraints weight = 44130.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146312 restraints weight = 22750.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149332 restraints weight = 15132.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.151121 restraints weight = 11897.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.151977 restraints weight = 10344.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  11204  Z= 0.154
  Angle     :  0.563   7.329  15209  Z= 0.295
  Chirality :  0.038   0.150   1666
  Planarity :  0.004   0.051   1914
  Dihedral  : 10.399 121.101   1654
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.63 %
    Favored  : 87.75 %
  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: -3.46 (0.21), residues: 1325
  helix: -1.64 (0.21), residues: 494
  sheet: -2.70 (0.37), residues: 142
  loop : -2.75 (0.22), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 249 
 TYR   0.019   0.001   TYR B  24 
 PHE   0.009   0.001   PHE B 357 
 TRP   0.017   0.001   TRP B 580 
 HIS   0.003   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11204)
  covalent geometry    : angle       0.56345 (15209)
  hydrogen bonds       : bond        0.04723 (  305)
  hydrogen bonds       : angle       5.21106 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 181
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   90 ASP cc_start: 0.7743 (t0) cc_final: 0.7456 (t0)
REVERT: B   65 GLN cc_start: 0.7692 (pt0) cc_final: 0.7300 (pp30)
REVERT: B  124 GLN cc_start: 0.8259 (pp30) cc_final: 0.7853 (pt0)
REVERT: B  150 PHE cc_start: 0.7715 (m-80) cc_final: 0.7514 (m-80)
REVERT: B  284 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7944 (t0)
REVERT: B  411 MET cc_start: 0.4288 (mmm) cc_final: 0.4002 (mmm)
REVERT: A  496 ARG cc_start: 0.7585 (mpp80) cc_final: 0.7338 (mtm180)
REVERT: A  501 TYR cc_start: 0.8497 (m-80) cc_final: 0.8099 (m-80)
REVERT: C   90 MET cc_start: 0.7586 (mmt) cc_final: 0.7026 (mmp)
  outliers start: 19
  outliers final: 11
  residues processed: 192
  average time/residue: 0.2781
  time to fit residues: 73.0344
Evaluate side-chains
  185 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0980
   chunk 102 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 313 GLN
** C  42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 102 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.169209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.138580 restraints weight = 44346.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.143432 restraints weight = 23040.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.146465 restraints weight = 15401.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.148221 restraints weight = 12181.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148770 restraints weight = 10594.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  11204  Z= 0.175
  Angle     :  0.569   6.641  15209  Z= 0.299
  Chirality :  0.039   0.140   1666
  Planarity :  0.004   0.055   1914
  Dihedral  : 10.397 116.495   1654
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.00 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.18 (0.21), residues: 1325
  helix: -1.24 (0.22), residues: 495
  sheet: -2.54 (0.38), residues: 146
  loop : -2.72 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 220 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.009   0.001   PHE B 495 
 TRP   0.015   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (11204)
  covalent geometry    : angle       0.56855 (15209)
  hydrogen bonds       : bond        0.04340 (  305)
  hydrogen bonds       : angle       5.12270 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  202 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.602 
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: O   90 ASP cc_start: 0.7787 (t0) cc_final: 0.7530 (t0)
REVERT: B   65 GLN cc_start: 0.7732 (pt0) cc_final: 0.7303 (pp30)
REVERT: B  227 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6722 (ptt)
REVERT: B  284 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (t0)
REVERT: B  411 MET cc_start: 0.4530 (mmm) cc_final: 0.4225 (mmm)
REVERT: B  554 ASP cc_start: 0.8228 (m-30) cc_final: 0.7608 (t0)
REVERT: A  496 ARG cc_start: 0.7626 (mpp80) cc_final: 0.7388 (mtm180)
REVERT: C   90 MET cc_start: 0.7554 (mmt) cc_final: 0.7094 (mmp)
  outliers start: 22
  outliers final: 16
  residues processed: 191
  average time/residue: 0.2781
  time to fit residues: 73.0178
Evaluate side-chains
  192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  284 ASN
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  630 ASP
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 123 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 105 optimal weight:    2.9990
   chunk 124 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
C  42 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.169844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139485 restraints weight = 44371.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.144214 restraints weight = 23072.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147193 restraints weight = 15556.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148935 restraints weight = 12336.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.149630 restraints weight = 10714.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11204  Z= 0.140
  Angle     :  0.542   6.531  15209  Z= 0.284
  Chirality :  0.038   0.137   1666
  Planarity :  0.004   0.056   1914
  Dihedral  : 10.314 112.799   1654
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 13.20 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.92 (0.22), residues: 1325
  helix: -0.87 (0.23), residues: 503
  sheet: -2.42 (0.38), residues: 146
  loop : -2.73 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O  72 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.024   0.001   PHE B 333 
 TRP   0.015   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11204)
  covalent geometry    : angle       0.54218 (15209)
  hydrogen bonds       : bond        0.03924 (  305)
  hydrogen bonds       : angle       4.88122 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   90 ASP cc_start: 0.7795 (t0) cc_final: 0.7550 (t0)
REVERT: B   65 GLN cc_start: 0.7704 (pt0) cc_final: 0.7288 (pp30)
REVERT: B  124 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8274 (pp30)
REVERT: B  343 MET cc_start: 0.8937 (mmt) cc_final: 0.8344 (mmt)
REVERT: B  411 MET cc_start: 0.4436 (mmm) cc_final: 0.4168 (mmm)
REVERT: B  554 ASP cc_start: 0.8238 (m-30) cc_final: 0.7729 (t0)
REVERT: A  496 ARG cc_start: 0.7646 (mpp80) cc_final: 0.7426 (mtm180)
REVERT: C   90 MET cc_start: 0.7790 (mmt) cc_final: 0.7340 (mmp)
  outliers start: 24
  outliers final: 21
  residues processed: 188
  average time/residue: 0.2717
  time to fit residues: 70.3853
Evaluate side-chains
  188 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain C residue   42 ASN
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 131 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 112 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 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 = 0.3995 r_free = 0.3995 target = 0.168851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.138790 restraints weight = 44652.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.143291 restraints weight = 23038.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.146304 restraints weight = 15542.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147998 restraints weight = 12288.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.149065 restraints weight = 10719.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  11204  Z= 0.156
  Angle     :  0.552   6.325  15209  Z= 0.288
  Chirality :  0.038   0.137   1666
  Planarity :  0.004   0.058   1914
  Dihedral  : 10.286 109.524   1654
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.58 %
    Favored  : 90.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.71 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.22), residues: 1325
  helix: -0.73 (0.23), residues: 509
  sheet: -2.29 (0.38), residues: 158
  loop : -2.75 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.024   0.001   PHE B 333 
 TRP   0.015   0.001   TRP B 580 
 HIS   0.003   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11204)
  covalent geometry    : angle       0.55208 (15209)
  hydrogen bonds       : bond        0.03897 (  305)
  hydrogen bonds       : angle       4.88094 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  198 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 170
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   90 ASP cc_start: 0.7836 (t0) cc_final: 0.7571 (t0)
REVERT: B   65 GLN cc_start: 0.7733 (pt0) cc_final: 0.7276 (pp30)
REVERT: B  124 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (pp30)
REVERT: B  227 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6712 (ptt)
REVERT: B  343 MET cc_start: 0.8945 (mmt) cc_final: 0.8270 (mmt)
REVERT: B  411 MET cc_start: 0.4348 (mmm) cc_final: 0.4103 (mmm)
REVERT: B  554 ASP cc_start: 0.8329 (m-30) cc_final: 0.7739 (t0)
REVERT: A  496 ARG cc_start: 0.7676 (mpp80) cc_final: 0.7441 (mtm180)
REVERT: A  661 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6890 (mm-30)
REVERT: C   90 MET cc_start: 0.7796 (mmt) cc_final: 0.7410 (mmp)
  outliers start: 28
  outliers final: 21
  residues processed: 187
  average time/residue: 0.2703
  time to fit residues: 69.5691
Evaluate side-chains
  192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 169
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  227 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 11 optimal weight:    0.1980
   chunk 72 optimal weight:    6.9990
   chunk 122 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 123 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 125 optimal weight:    9.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 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 = 0.3997 r_free = 0.3997 target = 0.169061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.138895 restraints weight = 44363.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.143630 restraints weight = 23110.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.146572 restraints weight = 15570.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.148256 restraints weight = 12316.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.149000 restraints weight = 10751.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11204  Z= 0.150
  Angle     :  0.549   6.056  15209  Z= 0.287
  Chirality :  0.038   0.136   1666
  Planarity :  0.004   0.057   1914
  Dihedral  : 10.257 105.716   1654
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.40 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.69 (0.22), residues: 1325
  helix: -0.58 (0.23), residues: 507
  sheet: -2.18 (0.37), residues: 170
  loop : -2.72 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.025   0.001   PHE B 333 
 TRP   0.014   0.001   TRP B 580 
 HIS   0.003   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (11204)
  covalent geometry    : angle       0.54858 (15209)
  hydrogen bonds       : bond        0.03768 (  305)
  hydrogen bonds       : angle       4.80662 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.578 
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: O   90 ASP cc_start: 0.7827 (t0) cc_final: 0.7581 (t0)
REVERT: B   65 GLN cc_start: 0.7720 (pt0) cc_final: 0.7272 (pp30)
REVERT: B  124 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8221 (pp30)
REVERT: B  343 MET cc_start: 0.9024 (mmt) cc_final: 0.8339 (mmt)
REVERT: B  441 LEU cc_start: 0.9120 (mt) cc_final: 0.8893 (mt)
REVERT: B  554 ASP cc_start: 0.8295 (m-30) cc_final: 0.7742 (t0)
REVERT: A  496 ARG cc_start: 0.7687 (mpp80) cc_final: 0.7433 (mtm180)
REVERT: A  661 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6924 (mm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 191
  average time/residue: 0.2677
  time to fit residues: 70.3807
Evaluate side-chains
  193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 101 optimal weight:    8.9990
   chunk 127 optimal weight:    6.9990
   chunk 125 optimal weight:    5.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
B 225 ASN
A 535 HIS
** C  42 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 = 0.3995 r_free = 0.3995 target = 0.168784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140382 restraints weight = 44610.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.143022 restraints weight = 24777.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145586 restraints weight = 16927.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145649 restraints weight = 15060.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.145957 restraints weight = 13604.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11204  Z= 0.149
  Angle     :  0.552   5.730  15209  Z= 0.289
  Chirality :  0.038   0.135   1666
  Planarity :  0.004   0.057   1914
  Dihedral  : 10.229 101.474   1654
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.17 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.22), residues: 1325
  helix: -0.48 (0.23), residues: 509
  sheet: -2.12 (0.38), residues: 170
  loop : -2.68 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  62 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.022   0.001   PHE B 333 
 TRP   0.014   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11204)
  covalent geometry    : angle       0.55229 (15209)
  hydrogen bonds       : bond        0.03717 (  305)
  hydrogen bonds       : angle       4.75460 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  200 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O   90 ASP cc_start: 0.7885 (t0) cc_final: 0.7642 (t0)
REVERT: B   65 GLN cc_start: 0.7721 (pt0) cc_final: 0.7267 (pp30)
REVERT: B  554 ASP cc_start: 0.8261 (m-30) cc_final: 0.7708 (t0)
REVERT: A  374 MET cc_start: 0.7943 (ttt) cc_final: 0.7698 (tpp)
REVERT: A  496 ARG cc_start: 0.7708 (mpp80) cc_final: 0.7438 (mtm180)
REVERT: A  661 GLU cc_start: 0.7554 (mm-30) cc_final: 0.6875 (mm-30)
  outliers start: 24
  outliers final: 24
  residues processed: 189
  average time/residue: 0.2629
  time to fit residues: 68.3437
Evaluate side-chains
  194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  547 ASP
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 119 optimal weight:    0.5980
   chunk 115 optimal weight:    0.6980
   chunk 83 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 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 = 0.4001 r_free = 0.4001 target = 0.169439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139911 restraints weight = 44563.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.144312 restraints weight = 22769.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147316 restraints weight = 15389.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.149066 restraints weight = 12161.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.149856 restraints weight = 10558.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11204  Z= 0.129
  Angle     :  0.541   7.138  15209  Z= 0.282
  Chirality :  0.038   0.135   1666
  Planarity :  0.004   0.056   1914
  Dihedral  : 10.155  96.968   1654
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.17 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.23), residues: 1325
  helix: -0.28 (0.24), residues: 506
  sheet: -1.98 (0.38), residues: 168
  loop : -2.61 (0.23), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 583 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.023   0.001   PHE B 333 
 TRP   0.013   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (11204)
  covalent geometry    : angle       0.54147 (15209)
  hydrogen bonds       : bond        0.03511 (  305)
  hydrogen bonds       : angle       4.62643 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  195 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 172
  time to evaluate  : 0.520 
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: O   90 ASP cc_start: 0.7839 (t0) cc_final: 0.7583 (t0)
REVERT: B   65 GLN cc_start: 0.7688 (pt0) cc_final: 0.7224 (pp30)
REVERT: B  554 ASP cc_start: 0.8304 (m-30) cc_final: 0.7755 (t0)
REVERT: A  496 ARG cc_start: 0.7669 (mpp80) cc_final: 0.7407 (mtm180)
REVERT: A  661 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6852 (mm-30)
  outliers start: 23
  outliers final: 23
  residues processed: 184
  average time/residue: 0.2653
  time to fit residues: 67.5119
Evaluate side-chains
  194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  523 MET
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 112 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 123 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 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 = 0.3995 r_free = 0.3995 target = 0.168969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.138632 restraints weight = 44549.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.143431 restraints weight = 23167.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146438 restraints weight = 15584.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.148179 restraints weight = 12311.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.148738 restraints weight = 10721.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11204  Z= 0.148
  Angle     :  0.559   8.051  15209  Z= 0.292
  Chirality :  0.038   0.135   1666
  Planarity :  0.004   0.056   1914
  Dihedral  : 10.156  94.042   1654
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.28 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.34 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.22), residues: 1325
  helix: -0.24 (0.24), residues: 506
  sheet: -1.97 (0.39), residues: 156
  loop : -2.64 (0.23), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.024   0.001   PHE B 574 
 TRP   0.013   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (11204)
  covalent geometry    : angle       0.55866 (15209)
  hydrogen bonds       : bond        0.03644 (  305)
  hydrogen bonds       : angle       4.68216 (  849)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   87 is missing expected H atoms. Skipping.
Residue TYR  114 is missing expected H atoms. Skipping.
Residue MET  507 is missing expected H atoms. Skipping.
Residue LYS  603 is missing expected H atoms. Skipping.
Residue LYS  605 is missing expected H atoms. Skipping.
Residue MET  607 is missing expected H atoms. Skipping.
Residue LYS  609 is missing expected H atoms. Skipping.
Residue LYS  626 is missing expected H atoms. Skipping.
Evaluate side-chains
  194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.503 
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: O   90 ASP cc_start: 0.7850 (t0) cc_final: 0.7605 (t0)
REVERT: B   65 GLN cc_start: 0.7711 (pt0) cc_final: 0.7225 (pp30)
REVERT: B  554 ASP cc_start: 0.8271 (m-30) cc_final: 0.7734 (t0)
REVERT: A  496 ARG cc_start: 0.7675 (mpp80) cc_final: 0.7408 (mtm180)
REVERT: A  661 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6862 (mm-30)
  outliers start: 22
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2670
  time to fit residues: 67.7482
Evaluate side-chains
  194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   64 VAL
Chi-restraints excluded: chain B residue    7 LEU
Chi-restraints excluded: chain B residue   24 TYR
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue   55 TRP
Chi-restraints excluded: chain B residue  107 CYS
Chi-restraints excluded: chain B residue  124 GLN
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  301 THR
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  566 THR
Chi-restraints excluded: chain B residue  629 ASN
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  297 HIS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  652 SER
Chi-restraints excluded: chain C residue  111 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 128 optimal weight:    9.9990
   chunk 5 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0980
   chunk 132 optimal weight:    7.9990
   chunk 114 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C  42 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 = 0.4031 r_free = 0.4031 target = 0.172334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.142821 restraints weight = 44198.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147412 restraints weight = 22502.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.150433 restraints weight = 15120.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152174 restraints weight = 11944.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.153162 restraints weight = 10375.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11204  Z= 0.096
  Angle     :  0.524   8.556  15209  Z= 0.271
  Chirality :  0.037   0.140   1666
  Planarity :  0.004   0.055   1914
  Dihedral  :  9.986  90.117   1654
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.02 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.10 (0.23), residues: 1325
  helix:  0.07 (0.24), residues: 508
  sheet: -1.89 (0.38), residues: 168
  loop : -2.51 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.018   0.001   TYR B  24 
 PHE   0.026   0.001   PHE B 333 
 TRP   0.013   0.001   TRP B 580 
 HIS   0.004   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 (11204)
  covalent geometry    : angle       0.52447 (15209)
  hydrogen bonds       : bond        0.03112 (  305)
  hydrogen bonds       : angle       4.35035 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3574.96 seconds
wall clock time: 61 minutes 40.66 seconds (3700.66 seconds total)