Starting phenix.real_space_refine
on Wed Feb  4 13:37:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jqx_61742/02_2026/9jqx_61742.cif"
  }
  resolution = 3.61
  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=   0.007 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      65      5.16       5
     Cl      2      4.86       5
     C    6968      2.51       5
     N    1793      2.21       5
     O    1940      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10769
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 695, 5512
          Classifications: {'peptide': 695}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 25, 'TRANS': 669}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 5232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 5232
          Classifications: {'peptide': 661}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 23, 'TRANS': 637}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'2BV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.70, per 1000 atoms: 0.25
  Number of scatterers: 10769
  At special positions: 0
  Unit cell: (73.47, 98.58, 163.68, 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)
     Cl      2     17.00
     S      65     16.00
     P       1     15.00
     O    1940      8.00
     N    1793      7.00
     C    6968      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 281 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 540 " - pdb=" SG  CYS A 637 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 519 " - pdb=" SG  CYS B 614 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 473.3 milliseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 8 sheets defined
      54.9% alpha, 11.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 70
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 115 through 127
      removed outlier: 3.915A  pdb=" N   ALA A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 4.274A  pdb=" N   ASP A 145 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 161
    Processing helix  chain 'A' and resid 162 through 173
    Processing helix  chain 'A' and resid 187 through 201
      removed outlier: 3.595A  pdb=" N   GLU A 201 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 236 through 246
      removed outlier: 3.638A  pdb=" N   ARG A 242 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 289
      removed outlier: 3.653A  pdb=" N   ALA A 289 " --> pdb=" O   GLN A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 326
      removed outlier: 3.511A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 329
      No H-bonds generated for 'chain 'A' and resid 327 through 329'
    Processing helix  chain 'A' and resid 331 through 335
    Processing helix  chain 'A' and resid 343 through 366
    Processing helix  chain 'A' and resid 379 through 392
      removed outlier: 3.590A  pdb=" N   ALA A 383 " --> pdb=" O   ASP A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 490
    Processing helix  chain 'A' and resid 491 through 494
      removed outlier: 4.219A  pdb=" N   LYS A 494 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 491 through 494'
    Processing helix  chain 'A' and resid 496 through 501
    Processing helix  chain 'A' and resid 503 through 525
      removed outlier: 3.577A  pdb=" N   ASN A 507 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A 525 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 559
      removed outlier: 3.643A  pdb=" N   ILE A 539 " --> pdb=" O   GLU A 535 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 544 " --> pdb=" O   CYS A 540 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ALA A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 572
    Processing helix  chain 'A' and resid 582 through 607
      removed outlier: 4.291A  pdb=" N   MET A 588 " --> pdb=" O   LYS A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 667
    Processing helix  chain 'A' and resid 679 through 702
      removed outlier: 5.280A  pdb=" N   ILE A 685 " --> pdb=" O   VAL A 681 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASN A 687 " --> pdb=" O   MET A 683 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA A 696 " --> pdb=" O   CYS A 692 " (cutoff:3.500A)
      Proline residue:  A 697  - end of helix
      removed outlier: 3.536A  pdb=" N   MET A 700 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 701 " --> pdb=" O   PRO A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 737
      removed outlier: 3.654A  pdb=" N   PHE A 710 " --> pdb=" O   GLN A 706 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL A 717 " --> pdb=" O   VAL A 713 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER A 724 " --> pdb=" O   CYS A 720 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   MET A 725 " --> pdb=" O   CYS A 721 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ILE A 728 " --> pdb=" O   SER A 724 " (cutoff:3.500A)
      Proline residue:  A 731  - end of helix
    Processing helix  chain 'B' and resid 46 through 51
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 85 through 99
      removed outlier: 3.588A  pdb=" N   VAL B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 123
      Proline residue:  B 117  - end of helix
      removed outlier: 3.789A  pdb=" N   LYS B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 156
    Processing helix  chain 'B' and resid 157 through 168
      removed outlier: 3.821A  pdb=" N   ARG B 161 " --> pdb=" O   PHE B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 183
    Processing helix  chain 'B' and resid 184 through 194
    Processing helix  chain 'B' and resid 210 through 221
      removed outlier: 4.342A  pdb=" N   SER B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS B 221 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 245
    Processing helix  chain 'B' and resid 263 through 267
    Processing helix  chain 'B' and resid 274 through 283
      removed outlier: 4.823A  pdb=" N   THR B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ALA B 281 " --> pdb=" O   GLU B 277 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU B 282 " --> pdb=" O   ILE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 318
      removed outlier: 4.323A  pdb=" N   GLY B 318 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 346
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 3.512A  pdb=" N   SER B 362 " --> pdb=" O   LYS B 358 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 471
      removed outlier: 3.561A  pdb=" N   TYR B 448 " --> pdb=" O   ASN B 444 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER B 451 " --> pdb=" O   ILE B 447 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS B 471 " --> pdb=" O   ALA B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 480
    Processing helix  chain 'B' and resid 482 through 505
    Processing helix  chain 'B' and resid 511 through 513
      No H-bonds generated for 'chain 'B' and resid 511 through 513'
    Processing helix  chain 'B' and resid 514 through 548
      removed outlier: 3.752A  pdb=" N   ILE B 525 " --> pdb=" O   ALA B 521 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU B 526 " --> pdb=" O   ARG B 522 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   MET B 537 " --> pdb=" O   SER B 533 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS B 540 " --> pdb=" O   ALA B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 585
      removed outlier: 3.765A  pdb=" N   GLY B 568 " --> pdb=" O   PHE B 564 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP B 574 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ILE B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA B 584 " --> pdb=" O   THR B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 644
    Processing helix  chain 'B' and resid 654 through 679
    Processing helix  chain 'B' and resid 682 through 705
      removed outlier: 5.021A  pdb=" N   PHE B 692 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   PHE B 693 " --> pdb=" O   LEU B 689 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL B 705 " --> pdb=" O   THR B 701 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 86
      removed outlier: 6.361A  pdb=" N   ILE A  39 " --> pdb=" O   HIS A  83 " (cutoff:3.500A)
      removed outlier: 8.405A  pdb=" N   ASN A  85 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLY A  41 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   MET A 110 " --> pdb=" O   HIS A  38 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU A 111 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   VAL A 133 " --> pdb=" O   PHE A 153 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 211
      removed outlier: 6.272A  pdb=" N   VAL A 178 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   THR A 208 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   ARG A 177 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 177 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA A 179 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   LEU A 181 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE A 231 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ILE A 262 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   GLY A 233 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR A 296 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   GLN A 418 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   LYS A 426 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASN A 436 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 397
    Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 461
      removed outlier: 6.366A  pdb=" N   ILE A 456 " --> pdb=" O   LYS A 629 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ARG A 631 " --> pdb=" O   ILE A 456 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   THR A 458 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   GLU A 633 " --> pdb=" O   THR A 458 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL A 460 " --> pdb=" O   GLU A 633 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 81
      removed outlier: 6.609A  pdb=" N   VAL B  31 " --> pdb=" O   HIS B  76 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   TRP B  78 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ILE B  33 " --> pdb=" O   TRP B  78 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   ASN B  80 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   GLY B  35 " --> pdb=" O   ASN B  80 " (cutoff:3.500A)
      removed outlier: 7.782A  pdb=" N   TYR B  32 " --> pdb=" O   MET B 105 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   PHE B 107 " --> pdb=" O   TYR B  32 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA B  34 " --> pdb=" O   PHE B 107 " (cutoff:3.500A)
      removed outlier: 8.750A  pdb=" N   LEU B 130 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LEU B 106 " --> pdb=" O   LEU B 130 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   GLN B 129 " --> pdb=" O   PHE B 148 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 207
      removed outlier: 7.343A  pdb=" N   VAL B 173 " --> pdb=" O   GLU B 203 " (cutoff:3.500A)
      removed outlier: 8.884A  pdb=" N   GLN B 205 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   THR B 175 " --> pdb=" O   GLN B 205 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   PHE B 207 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   TYR B 177 " --> pdb=" O   PHE B 207 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   ILE B 225 " --> pdb=" O   ARG B 172 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   TRP B 254 " --> pdb=" O   ILE B 286 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   VAL B 288 " --> pdb=" O   TRP B 254 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE B 256 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 9.006A  pdb=" N   LEU B 290 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ILE B 391 " --> pdb=" O   GLU B 406 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   GLU B 406 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ILE B 393 " --> pdb=" O   ILE B 404 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 375
    Processing sheet with id=AA8, first strand: chain 'B' and resid 589 through 593
      removed outlier: 3.670A  pdb=" N   GLU B 590 " --> pdb=" O   TYR B 613 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR B 613 " --> pdb=" O   GLU B 590 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS B 592 " --> pdb=" O   ASN B 611 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.37

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3412
        1.34 -     1.47: 2842
        1.47 -     1.60: 4672
        1.60 -     1.73: 0
        1.73 -     1.86: 106
  Bond restraints: 11032
  Sorted by residual:
  bond pdb=" CA  VAL A 681 "
       pdb=" C   VAL A 681 "
    ideal  model  delta    sigma   weight residual
    1.523  1.456  0.067 1.27e-02 6.20e+03 2.78e+01
  bond pdb=" CA  VAL A 681 "
       pdb=" CB  VAL A 681 "
    ideal  model  delta    sigma   weight residual
    1.540  1.489  0.052 1.36e-02 5.41e+03 1.44e+01
  bond pdb=" C   VAL A 232 "
       pdb=" N   GLY A 233 "
    ideal  model  delta    sigma   weight residual
    1.331  1.355 -0.024 6.60e-03 2.30e+04 1.32e+01
  bond pdb=" N   MET A 683 "
       pdb=" CA  MET A 683 "
    ideal  model  delta    sigma   weight residual
    1.459  1.417  0.043 1.21e-02 6.83e+03 1.24e+01
  bond pdb=" CG  LEU B 634 "
       pdb=" CD1 LEU B 634 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.15e+00
  ... (remaining 11027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.34: 14906
        3.34 -     6.67: 78
        6.67 -    10.01: 11
       10.01 -    13.34: 0
       13.34 -    16.68: 1
  Bond angle restraints: 14996
  Sorted by residual:
  angle pdb=" N   MET A 683 "
        pdb=" CA  MET A 683 "
        pdb=" C   MET A 683 "
      ideal   model   delta    sigma   weight residual
     111.28  102.94    8.34 1.09e+00 8.42e-01 5.85e+01
  angle pdb=" N   GLY A 682 "
        pdb=" CA  GLY A 682 "
        pdb=" C   GLY A 682 "
      ideal   model   delta    sigma   weight residual
     113.18   96.50   16.68 2.37e+00 1.78e-01 4.95e+01
  angle pdb=" CA  ASN B  72 "
        pdb=" CB  ASN B  72 "
        pdb=" CG  ASN B  72 "
      ideal   model   delta    sigma   weight residual
     112.60  117.20   -4.60 1.00e+00 1.00e+00 2.12e+01
  angle pdb=" N   ARG A 679 "
        pdb=" CA  ARG A 679 "
        pdb=" C   ARG A 679 "
      ideal   model   delta    sigma   weight residual
     113.41  108.14    5.27 1.22e+00 6.72e-01 1.87e+01
  angle pdb=" C   VAL A 681 "
        pdb=" CA  VAL A 681 "
        pdb=" CB  VAL A 681 "
      ideal   model   delta    sigma   weight residual
     111.29  104.22    7.07 1.64e+00 3.72e-01 1.86e+01
  ... (remaining 14991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.15: 5768
       23.15 -    46.29: 647
       46.29 -    69.44: 69
       69.44 -    92.58: 20
       92.58 -   115.73: 2
  Dihedral angle restraints: 6506
    sinusoidal: 2544
      harmonic: 3962
  Sorted by residual:
  dihedral pdb=" CB  CYS A 540 "
           pdb=" SG  CYS A 540 "
           pdb=" SG  CYS A 637 "
           pdb=" CB  CYS A 637 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.11  -78.11     1      1.00e+01 1.00e-02 7.62e+01
  dihedral pdb=" CA  VAL B 707 "
           pdb=" C   VAL B 707 "
           pdb=" N   PRO B 708 "
           pdb=" CA  PRO B 708 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.54  -22.46     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ARG A 225 "
           pdb=" C   ARG A 225 "
           pdb=" N   GLN A 226 "
           pdb=" CA  GLN A 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.83   22.17     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 6503 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.076: 1701
       1.076 -    2.153: 0
       2.153 -    3.229: 0
       3.229 -    4.306: 0
       4.306 -    5.382: 1
  Chirality restraints: 1702
  Sorted by residual:
  chirality pdb=" C13 2BV A 801 "
            pdb=" C12 2BV A 801 "
            pdb=" C14 2BV A 801 "
            pdb=" C18 2BV A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63   -2.76    5.38 2.00e-01 2.50e+01 7.24e+02
  chirality pdb=" CB  THR B 496 "
            pdb=" CA  THR B 496 "
            pdb=" OG1 THR B 496 "
            pdb=" CG2 THR B 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.28    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  ILE A 675 "
            pdb=" CA  ILE A 675 "
            pdb=" CG1 ILE A 675 "
            pdb=" CG2 ILE A 675 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1699 not shown)

  Planarity restraints: 1879
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 378 "   -0.039 5.00e-02 4.00e+02   5.96e-02 5.68e+00
        pdb=" N   PRO B 379 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 379 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 379 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 572 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ALA B 572 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ALA B 572 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 573 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 678 "    0.007 2.00e-02 2.50e+03   1.54e-02 2.37e+00
        pdb=" C   SER A 678 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   SER A 678 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ARG A 679 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1876 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 839
        2.74 -     3.28: 11186
        3.28 -     3.82: 18445
        3.82 -     4.36: 21402
        4.36 -     4.90: 36988
  Nonbonded interactions: 88860
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 663 "
            pdb=" OG1 THR A 667 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   ARG A 318 "
            pdb=" ND2 ASN A 322 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" O   ALA B 576 "
            pdb=" OG1 THR B 579 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   GLY A 137 "
            pdb=" O3  2BV A 801 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OG  SER A 116 "
            pdb=" O1  2BV A 801 "
     model   vdw
     2.227 3.040
  ... (remaining 88855 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:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.450
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:   13.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
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      :  0.004   0.082  11036  Z= 0.190
  Angle     :  0.657  16.678  15004  Z= 0.345
  Chirality :  0.137   5.382   1702
  Planarity :  0.004   0.060   1879
  Dihedral  : 18.077 115.728   3938
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  6.61 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 34.75 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.23), residues: 1346
  helix:  0.58 (0.21), residues: 689
  sheet: -1.03 (0.40), residues: 162
  loop : -1.80 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 476 
 TYR   0.014   0.001   TYR A 555 
 PHE   0.020   0.001   PHE B 548 
 TRP   0.017   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (11032)
  covalent geometry    : angle       0.65628 (14996)
  SS BOND              : bond        0.00284 (    4)
  SS BOND              : angle       0.99495 (    8)
  hydrogen bonds       : bond        0.14579 (  539)
  hydrogen bonds       : angle       6.43549 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 181
  time to evaluate  : 0.297 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 182
  average time/residue: 0.0957
  time to fit residues: 24.8631
Evaluate side-chains
  184 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 181
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  683 MET
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain B residue  618 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.1980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.110013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.092581 restraints weight = 19461.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.094443 restraints weight = 11720.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.095655 restraints weight = 8093.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.096447 restraints weight = 6144.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.096790 restraints weight = 5045.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.0945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11036  Z= 0.251
  Angle     :  0.657   9.390  15004  Z= 0.343
  Chirality :  0.044   0.160   1702
  Planarity :  0.004   0.050   1879
  Dihedral  :  5.849  51.574   1501
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.80 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 30.16 %
    Favored  : 65.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.23), residues: 1346
  helix:  0.52 (0.20), residues: 704
  sheet: -1.00 (0.40), residues: 156
  loop : -2.00 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 149 
 TYR   0.016   0.002   TYR B 629 
 PHE   0.023   0.002   PHE B 548 
 TRP   0.018   0.002   TRP B 581 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 (11032)
  covalent geometry    : angle       0.65615 (14996)
  SS BOND              : bond        0.00538 (    4)
  SS BOND              : angle       1.41031 (    8)
  hydrogen bonds       : bond        0.04599 (  539)
  hydrogen bonds       : angle       4.91039 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 197
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  356 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8433 (mp)
REVERT: B  267 VAL cc_start: 0.8418 (t) cc_final: 0.8189 (t)
  outliers start: 52
  outliers final: 27
  residues processed: 236
  average time/residue: 0.0887
  time to fit residues: 30.2901
Evaluate side-chains
  211 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 183
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 MET
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  354 ASP
Chi-restraints excluded: chain B residue  371 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  647 VAL
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 121 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0030
   chunk 81 optimal weight:    0.7980
   chunk 110 optimal weight:    8.9990
   chunk 113 optimal weight:    0.8980
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
B 205 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.112713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.095641 restraints weight = 19363.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.097468 restraints weight = 11479.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.098668 restraints weight = 7925.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.099475 restraints weight = 6036.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.099830 restraints weight = 4926.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11036  Z= 0.132
  Angle     :  0.598   9.586  15004  Z= 0.306
  Chirality :  0.042   0.196   1702
  Planarity :  0.004   0.042   1879
  Dihedral  :  5.208  49.947   1494
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 32.15 %
    Favored  : 64.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.70 (0.23), residues: 1346
  helix:  0.72 (0.20), residues: 695
  sheet: -1.20 (0.40), residues: 162
  loop : -1.91 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.014   0.001   TYR A 555 
 PHE   0.021   0.001   PHE B 548 
 TRP   0.013   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11032)
  covalent geometry    : angle       0.59762 (14996)
  SS BOND              : bond        0.00312 (    4)
  SS BOND              : angle       1.16268 (    8)
  hydrogen bonds       : bond        0.03937 (  539)
  hydrogen bonds       : angle       4.55445 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 199
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8455 (mp)
REVERT: B  267 VAL cc_start: 0.8431 (t) cc_final: 0.8185 (t)
  outliers start: 43
  outliers final: 27
  residues processed: 230
  average time/residue: 0.1010
  time to fit residues: 33.1045
Evaluate side-chains
  221 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 193
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  610 GLU
Chi-restraints excluded: chain B residue  647 VAL
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  679 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 115 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.111498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.094217 restraints weight = 19480.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.096123 restraints weight = 11677.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.097276 restraints weight = 8021.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.098105 restraints weight = 6131.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.098627 restraints weight = 4983.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11036  Z= 0.173
  Angle     :  0.616   9.339  15004  Z= 0.315
  Chirality :  0.043   0.210   1702
  Planarity :  0.004   0.043   1879
  Dihedral  :  5.241  54.499   1494
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 31.37 %
    Favored  : 63.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.23), residues: 1346
  helix:  0.71 (0.20), residues: 693
  sheet: -0.99 (0.40), residues: 154
  loop : -2.05 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 476 
 TYR   0.012   0.001   TYR A 555 
 PHE   0.023   0.001   PHE B 548 
 TRP   0.014   0.001   TRP B 581 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (11032)
  covalent geometry    : angle       0.61575 (14996)
  SS BOND              : bond        0.00396 (    4)
  SS BOND              : angle       1.18507 (    8)
  hydrogen bonds       : bond        0.03917 (  539)
  hydrogen bonds       : angle       4.53372 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 196
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: B  267 VAL cc_start: 0.8482 (t) cc_final: 0.8262 (t)
REVERT: B  386 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7095 (mt-10)
REVERT: B  577 ILE cc_start: 0.8277 (tt) cc_final: 0.7891 (mm)
REVERT: B  654 ASP cc_start: 0.6292 (p0) cc_final: 0.6030 (p0)
  outliers start: 57
  outliers final: 39
  residues processed: 239
  average time/residue: 0.0949
  time to fit residues: 32.3466
Evaluate side-chains
  233 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 192
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  354 ASP
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  386 GLU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  610 GLU
Chi-restraints excluded: chain B residue  618 HIS
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.2980
   chunk 19 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 94 optimal weight:    0.6980
   chunk 114 optimal weight:    5.9990
   chunk 123 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.113415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.096234 restraints weight = 19321.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.098134 restraints weight = 11571.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.099300 restraints weight = 7924.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.100144 restraints weight = 6037.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100705 restraints weight = 4900.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11036  Z= 0.123
  Angle     :  0.590   9.480  15004  Z= 0.300
  Chirality :  0.042   0.207   1702
  Planarity :  0.004   0.042   1879
  Dihedral  :  5.083  52.985   1494
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.89 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.23), residues: 1346
  helix:  0.82 (0.20), residues: 693
  sheet: -1.22 (0.39), residues: 160
  loop : -1.95 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 476 
 TYR   0.014   0.001   TYR A 555 
 PHE   0.022   0.001   PHE B 548 
 TRP   0.013   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11032)
  covalent geometry    : angle       0.58934 (14996)
  SS BOND              : bond        0.00303 (    4)
  SS BOND              : angle       1.12779 (    8)
  hydrogen bonds       : bond        0.03620 (  539)
  hydrogen bonds       : angle       4.39221 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 201
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8438 (mp)
REVERT: A  583 TRP cc_start: 0.7257 (p-90) cc_final: 0.7028 (p-90)
REVERT: B  267 VAL cc_start: 0.8444 (t) cc_final: 0.8190 (t)
REVERT: B  565 MET cc_start: 0.6855 (mmp) cc_final: 0.6080 (mtp)
REVERT: B  577 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: B  594 LEU cc_start: 0.7713 (mm) cc_final: 0.7313 (mm)
REVERT: B  654 ASP cc_start: 0.6155 (p0) cc_final: 0.5922 (p0)
  outliers start: 53
  outliers final: 39
  residues processed: 241
  average time/residue: 0.0895
  time to fit residues: 31.0488
Evaluate side-chains
  230 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 189
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  722 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  585 ASP
Chi-restraints excluded: chain B residue  610 GLU
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  679 LEU
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 125 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0670
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7120

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

Flipped N/Q/H residues before XYZ refinement:
B 253 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.113313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.096195 restraints weight = 19343.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.098047 restraints weight = 11534.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.099249 restraints weight = 7922.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.099965 restraints weight = 6018.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.100584 restraints weight = 4968.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11036  Z= 0.128
  Angle     :  0.592   9.426  15004  Z= 0.302
  Chirality :  0.042   0.227   1702
  Planarity :  0.003   0.041   1879
  Dihedral  :  5.042  54.345   1494
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 31.20 %
    Favored  : 63.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.23), residues: 1346
  helix:  0.83 (0.20), residues: 696
  sheet: -1.18 (0.40), residues: 159
  loop : -1.96 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.015   0.001   TYR A 555 
 PHE   0.021   0.001   PHE B 548 
 TRP   0.013   0.001   TRP A 264 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11032)
  covalent geometry    : angle       0.59172 (14996)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       1.09766 (    8)
  hydrogen bonds       : bond        0.03582 (  539)
  hydrogen bonds       : angle       4.34845 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 197
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: A  583 TRP cc_start: 0.7224 (p-90) cc_final: 0.7002 (p-90)
REVERT: B  267 VAL cc_start: 0.8434 (t) cc_final: 0.8203 (t)
REVERT: B  565 MET cc_start: 0.6843 (mmp) cc_final: 0.6102 (mtp)
REVERT: B  577 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7918 (mm)
REVERT: B  654 ASP cc_start: 0.6223 (p0) cc_final: 0.5972 (p0)
  outliers start: 57
  outliers final: 41
  residues processed: 243
  average time/residue: 0.0952
  time to fit residues: 33.4188
Evaluate side-chains
  235 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  177 ARG
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  685 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain A residue  722 PHE
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  202 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  610 GLU
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  679 LEU
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 82 optimal weight:    0.2980
   chunk 123 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.113554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.096220 restraints weight = 19272.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.098057 restraints weight = 11492.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099305 restraints weight = 7935.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.100120 restraints weight = 6029.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.100684 restraints weight = 4906.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11036  Z= 0.126
  Angle     :  0.599   9.597  15004  Z= 0.304
  Chirality :  0.042   0.227   1702
  Planarity :  0.003   0.039   1879
  Dihedral  :  5.009  54.389   1494
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 31.98 %
    Favored  : 63.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.59 (0.23), residues: 1346
  helix:  0.84 (0.20), residues: 698
  sheet: -1.17 (0.40), residues: 160
  loop : -1.93 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.015   0.001   TYR A 555 
 PHE   0.020   0.001   PHE B 548 
 TRP   0.013   0.001   TRP A 264 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (11032)
  covalent geometry    : angle       0.59821 (14996)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       1.13744 (    8)
  hydrogen bonds       : bond        0.03530 (  539)
  hydrogen bonds       : angle       4.31815 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 195
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  356 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8487 (mp)
REVERT: B   70 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7546 (pp)
REVERT: B  267 VAL cc_start: 0.8418 (t) cc_final: 0.8201 (t)
REVERT: B  565 MET cc_start: 0.6733 (mmp) cc_final: 0.6040 (mtp)
REVERT: B  577 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7989 (mm)
REVERT: B  594 LEU cc_start: 0.8105 (mm) cc_final: 0.7759 (mm)
REVERT: B  654 ASP cc_start: 0.6246 (p0) cc_final: 0.5989 (p0)
  outliers start: 50
  outliers final: 37
  residues processed: 233
  average time/residue: 0.0873
  time to fit residues: 29.0806
Evaluate side-chains
  229 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 189
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  452 GLN
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  386 GLU
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 66 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** B 611 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 = 0.3519 r_free = 0.3519 target = 0.111947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.094537 restraints weight = 19349.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.096377 restraints weight = 11628.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.097560 restraints weight = 8066.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098354 restraints weight = 6186.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.098876 restraints weight = 5063.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11036  Z= 0.172
  Angle     :  0.620   9.704  15004  Z= 0.316
  Chirality :  0.043   0.227   1702
  Planarity :  0.004   0.038   1879
  Dihedral  :  5.143  56.794   1494
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 31.63 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.23), residues: 1346
  helix:  0.80 (0.20), residues: 698
  sheet: -1.13 (0.40), residues: 159
  loop : -1.99 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 177 
 TYR   0.012   0.001   TYR B 629 
 PHE   0.019   0.001   PHE A 235 
 TRP   0.011   0.001   TRP A 352 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11032)
  covalent geometry    : angle       0.61935 (14996)
  SS BOND              : bond        0.00427 (    4)
  SS BOND              : angle       1.19985 (    8)
  hydrogen bonds       : bond        0.03721 (  539)
  hydrogen bonds       : angle       4.40071 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 183
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  356 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: B  149 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8119 (mtp180)
REVERT: B  267 VAL cc_start: 0.8437 (t) cc_final: 0.8223 (t)
REVERT: B  565 MET cc_start: 0.6707 (mmp) cc_final: 0.6015 (mtp)
REVERT: B  577 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8031 (mm)
REVERT: B  645 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7825 (ptp-170)
REVERT: B  654 ASP cc_start: 0.6270 (p0) cc_final: 0.6014 (p0)
  outliers start: 56
  outliers final: 43
  residues processed: 225
  average time/residue: 0.0888
  time to fit residues: 28.7326
Evaluate side-chains
  228 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 181
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ARG
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 115 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 104 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 205 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.112717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.095420 restraints weight = 19198.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.097320 restraints weight = 11675.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.098511 restraints weight = 7990.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.099309 restraints weight = 6059.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.099796 restraints weight = 4966.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11036  Z= 0.142
  Angle     :  0.608   9.685  15004  Z= 0.310
  Chirality :  0.042   0.232   1702
  Planarity :  0.003   0.040   1879
  Dihedral  :  5.095  56.337   1494
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 32.24 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.23), residues: 1346
  helix:  0.84 (0.20), residues: 698
  sheet: -1.13 (0.40), residues: 159
  loop : -1.98 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.013   0.001   TYR A 555 
 PHE   0.019   0.001   PHE B 548 
 TRP   0.012   0.001   TRP B 581 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (11032)
  covalent geometry    : angle       0.60714 (14996)
  SS BOND              : bond        0.00367 (    4)
  SS BOND              : angle       1.12159 (    8)
  hydrogen bonds       : bond        0.03614 (  539)
  hydrogen bonds       : angle       4.34265 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 186
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  356 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8470 (mp)
REVERT: B  149 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8050 (mtp180)
REVERT: B  267 VAL cc_start: 0.8423 (t) cc_final: 0.8206 (t)
REVERT: B  565 MET cc_start: 0.6738 (mmp) cc_final: 0.6047 (mtp)
REVERT: B  577 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7980 (mm)
REVERT: B  645 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7792 (ptp-170)
REVERT: B  654 ASP cc_start: 0.6230 (p0) cc_final: 0.5975 (p0)
  outliers start: 49
  outliers final: 38
  residues processed: 222
  average time/residue: 0.0915
  time to fit residues: 29.5227
Evaluate side-chains
  228 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 186
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ARG
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 120 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0010
   chunk 81 optimal weight:    0.6980
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.0988

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

Flipped N/Q/H residues before XYZ refinement:
B 390 ASN
B 410 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.112254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.094979 restraints weight = 19261.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.096863 restraints weight = 11587.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.098050 restraints weight = 7978.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.098815 restraints weight = 6082.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.099399 restraints weight = 4986.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11036  Z= 0.156
  Angle     :  0.622   9.634  15004  Z= 0.319
  Chirality :  0.043   0.242   1702
  Planarity :  0.004   0.040   1879
  Dihedral  :  5.153  58.575   1494
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 32.15 %
    Favored  : 63.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.23), residues: 1346
  helix:  0.83 (0.20), residues: 699
  sheet: -1.14 (0.41), residues: 159
  loop : -1.99 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.011   0.001   TYR B 448 
 PHE   0.019   0.001   PHE B 548 
 TRP   0.011   0.001   TRP A 264 
 HIS   0.006   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11032)
  covalent geometry    : angle       0.62176 (14996)
  SS BOND              : bond        0.00409 (    4)
  SS BOND              : angle       1.20186 (    8)
  hydrogen bonds       : bond        0.03670 (  539)
  hydrogen bonds       : angle       4.35999 ( 1572)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 186
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  224 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7452 (ptm160)
REVERT: A  356 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8428 (mp)
REVERT: B  149 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7954 (mtp180)
REVERT: B  267 VAL cc_start: 0.8469 (t) cc_final: 0.8261 (t)
REVERT: B  564 PHE cc_start: 0.6890 (p90) cc_final: 0.6622 (p90)
REVERT: B  565 MET cc_start: 0.6663 (mmp) cc_final: 0.6062 (mtp)
REVERT: B  577 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8162 (mm)
REVERT: B  645 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7804 (ptp-170)
REVERT: B  654 ASP cc_start: 0.6308 (p0) cc_final: 0.6039 (p0)
  outliers start: 51
  outliers final: 44
  residues processed: 225
  average time/residue: 0.0916
  time to fit residues: 30.0346
Evaluate side-chains
  232 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 184
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  190 SER
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  521 VAL
Chi-restraints excluded: chain A residue  522 ILE
Chi-restraints excluded: chain A residue  545 TRP
Chi-restraints excluded: chain A residue  559 PHE
Chi-restraints excluded: chain A residue  565 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  656 ILE
Chi-restraints excluded: chain A residue  709 SER
Chi-restraints excluded: chain A residue  720 CYS
Chi-restraints excluded: chain B residue   31 VAL
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  149 ARG
Chi-restraints excluded: chain B residue  150 VAL
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  274 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  372 SER
Chi-restraints excluded: chain B residue  390 ASN
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  437 TYR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  541 THR
Chi-restraints excluded: chain B residue  545 HIS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  645 ARG
Chi-restraints excluded: chain B residue  662 VAL
Chi-restraints excluded: chain B residue  679 LEU
Chi-restraints excluded: chain B residue  711 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 120 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 133 optimal weight:    9.9990
   chunk 63 optimal weight:    6.9990
   chunk 74 optimal weight:    0.3980
   chunk 113 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 611 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 = 0.3514 r_free = 0.3514 target = 0.111648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.094393 restraints weight = 19453.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.096270 restraints weight = 11643.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.097464 restraints weight = 7992.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.098279 restraints weight = 6091.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.098839 restraints weight = 4945.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11036  Z= 0.179
  Angle     :  0.637   9.755  15004  Z= 0.327
  Chirality :  0.043   0.238   1702
  Planarity :  0.004   0.040   1879
  Dihedral  :  5.213  59.761   1494
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 32.06 %
    Favored  : 63.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.23), residues: 1346
  helix:  0.82 (0.20), residues: 698
  sheet: -1.10 (0.41), residues: 158
  loop : -2.01 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 476 
 TYR   0.015   0.001   TYR B 448 
 PHE   0.021   0.001   PHE A 712 
 TRP   0.014   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (11032)
  covalent geometry    : angle       0.63678 (14996)
  SS BOND              : bond        0.00453 (    4)
  SS BOND              : angle       1.25572 (    8)
  hydrogen bonds       : bond        0.03746 (  539)
  hydrogen bonds       : angle       4.39534 ( 1572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1560.79 seconds
wall clock time: 27 minutes 52.10 seconds (1672.10 seconds total)