Starting phenix.real_space_refine
on Tue Mar  3 22:37:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxj_21440/03_2026/6vxj_21440.map"
  }
  resolution = 4.1
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5794      2.51       5
     N    1454      2.21       5
     O    1589      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8895
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 566, 4405
          Classifications: {'peptide': 566}
          Link IDs: {'PTRANS': 18, 'TRANS': 547}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 566, 4405
          Classifications: {'peptide': 566}
          Link IDs: {'PTRANS': 18, 'TRANS': 547}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'CLR': 1, 'RS4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.48, per 1000 atoms: 0.28
  Number of scatterers: 8895
  At special positions: 0
  Unit cell: (104.55, 77.49, 126.69, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1589      8.00
     N    1454      7.00
     C    5794      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS B 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 378.7 milliseconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      54.8% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 94
      removed outlier: 3.652A  pdb=" N   LEU A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 3.629A  pdb=" N   ASN A 120 " --> pdb=" O   ASN A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 4.164A  pdb=" N   SER A 143 " --> pdb=" O   ASN A 139 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG A 147 " --> pdb=" O   SER A 143 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 168
      removed outlier: 5.084A  pdb=" N   GLU A 159 " --> pdb=" O   HIS A 155 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ARG A 160 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN A 166 " --> pdb=" O   ASN A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 189
      No H-bonds generated for 'chain 'A' and resid 187 through 189'
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 3.528A  pdb=" N   THR A 194 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 232
      removed outlier: 4.280A  pdb=" N   VAL A 224 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 3.978A  pdb=" N   PHE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 273 through 278'
    Processing helix  chain 'A' and resid 289 through 294
    Processing helix  chain 'A' and resid 330 through 336
      removed outlier: 4.185A  pdb=" N   ILE A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TYR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.717A  pdb=" N   THR A 345 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 389
      removed outlier: 3.727A  pdb=" N   TRP A 379 " --> pdb=" O   HIS A 375 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 413
      removed outlier: 3.678A  pdb=" N   GLN A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 4.027A  pdb=" N   THR A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
      removed outlier: 3.519A  pdb=" N   VAL A 445 " --> pdb=" O   VAL A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 461
      removed outlier: 3.849A  pdb=" N   GLU A 458 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
      removed outlier: 3.583A  pdb=" N   LEU A 474 " --> pdb=" O   PHE A 470 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 498
      removed outlier: 4.174A  pdb=" N   CYS A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE A 492 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   PHE A 495 " --> pdb=" O   CYS A 491 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   MET A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 527
      removed outlier: 3.500A  pdb=" N   PHE A 511 " --> pdb=" O   PHE A 507 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   MET A 514 " --> pdb=" O   MET A 510 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 527 " --> pdb=" O   MET A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 551
      removed outlier: 4.082A  pdb=" N   PHE A 547 " --> pdb=" O   ILE A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.570A  pdb=" N   ILE A 561 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 570
    Processing helix  chain 'A' and resid 572 through 584
      removed outlier: 4.224A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN A 584 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 617
      removed outlier: 3.514A  pdb=" N   VAL A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 650
      removed outlier: 3.615A  pdb=" N   LEU A 626 " --> pdb=" O   SER A 622 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TRP A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 639 " --> pdb=" O   CYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
      removed outlier: 3.652A  pdb=" N   LEU B  90 " --> pdb=" O   LYS B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 121
      removed outlier: 3.629A  pdb=" N   ASN B 120 " --> pdb=" O   ASN B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 4.165A  pdb=" N   SER B 143 " --> pdb=" O   ASN B 139 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B 144 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 146 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 168
      removed outlier: 5.084A  pdb=" N   GLU B 159 " --> pdb=" O   HIS B 155 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ARG B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN B 166 " --> pdb=" O   ASN B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 189
      No H-bonds generated for 'chain 'B' and resid 187 through 189'
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 3.529A  pdb=" N   THR B 194 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 232
      removed outlier: 4.281A  pdb=" N   VAL B 224 " --> pdb=" O   THR B 220 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 273 through 278
      removed outlier: 3.978A  pdb=" N   PHE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLU B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 273 through 278'
    Processing helix  chain 'B' and resid 289 through 294
    Processing helix  chain 'B' and resid 330 through 336
      removed outlier: 4.185A  pdb=" N   ILE B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   TYR B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 352
      removed outlier: 3.718A  pdb=" N   THR B 345 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 389
      removed outlier: 3.726A  pdb=" N   TRP B 379 " --> pdb=" O   HIS B 375 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 413
      removed outlier: 3.679A  pdb=" N   GLN B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 440
      removed outlier: 4.027A  pdb=" N   THR B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 445
      removed outlier: 3.519A  pdb=" N   VAL B 445 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 461
      removed outlier: 3.849A  pdb=" N   GLU B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 478
      removed outlier: 3.583A  pdb=" N   LEU B 474 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   SER B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 498
      removed outlier: 4.174A  pdb=" N   CYS B 491 " --> pdb=" O   ILE B 487 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 492 " --> pdb=" O   ILE B 488 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   PHE B 495 " --> pdb=" O   CYS B 491 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   MET B 496 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 527
      removed outlier: 3.641A  pdb=" N   MET B 514 " --> pdb=" O   MET B 510 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE B 527 " --> pdb=" O   MET B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 551
      removed outlier: 4.080A  pdb=" N   PHE B 547 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.570A  pdb=" N   ILE B 561 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 570
    Processing helix  chain 'B' and resid 572 through 584
      removed outlier: 4.224A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASN B 584 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 617
      removed outlier: 3.514A  pdb=" N   VAL B 615 " --> pdb=" O   GLU B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 650
      removed outlier: 3.616A  pdb=" N   LEU B 626 " --> pdb=" O   SER B 622 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TRP B 627 " --> pdb=" O   PRO B 623 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 639 " --> pdb=" O   CYS B 635 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70
      removed outlier: 6.818A  pdb=" N   SER A  65 " --> pdb=" O   CYS A  43 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   CYS A  43 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ILE A  67 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP A 105 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124
      removed outlier: 6.309A  pdb=" N   GLY A 122 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU A  75 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   THR A 257 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ALA A  77 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  79 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ALA A 260 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   LEU A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 70
      removed outlier: 6.817A  pdb=" N   SER B  65 " --> pdb=" O   CYS B  43 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   CYS B  43 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ILE B  67 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP B 105 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124
      removed outlier: 6.309A  pdb=" N   GLY B 122 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU B  75 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   THR B 257 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ALA B  77 " --> pdb=" O   THR B 257 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   LEU B 259 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ALA B 260 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   LEU B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)

    365 hydrogen bonds defined for protein.
    1059 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: 1.51

  Time building geometry restraints manager: 1.05 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: 2621
        1.34 -     1.45: 1656
        1.45 -     1.57: 4718
        1.57 -     1.69: 0
        1.69 -     1.81: 94
  Bond restraints: 9089
  Sorted by residual:
  bond pdb=" C28 RS4 B 701 "
       pdb=" O29 RS4 B 701 "
    ideal  model  delta    sigma   weight residual
    1.324  1.444 -0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" C10 RS4 B 701 "
       pdb=" C9  RS4 B 701 "
    ideal  model  delta    sigma   weight residual
    1.367  1.478 -0.111 2.00e-02 2.50e+03 3.10e+01
  bond pdb=" C20 RS4 B 701 "
       pdb=" C21 RS4 B 701 "
    ideal  model  delta    sigma   weight residual
    1.365  1.474 -0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" C   LEU B 479 "
       pdb=" N   PRO B 480 "
    ideal  model  delta    sigma   weight residual
    1.337  1.375 -0.038 1.06e-02 8.90e+03 1.32e+01
  bond pdb=" C   LEU A 479 "
       pdb=" N   PRO A 480 "
    ideal  model  delta    sigma   weight residual
    1.337  1.375 -0.038 1.06e-02 8.90e+03 1.31e+01
  ... (remaining 9084 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 11531
        1.88 -     3.77: 661
        3.77 -     5.65: 94
        5.65 -     7.54: 22
        7.54 -     9.42: 10
  Bond angle restraints: 12318
  Sorted by residual:
  angle pdb=" N   PRO B 485 "
        pdb=" CA  PRO B 485 "
        pdb=" C   PRO B 485 "
      ideal   model   delta    sigma   weight residual
     114.68  108.93    5.75 1.28e+00 6.10e-01 2.02e+01
  angle pdb=" N   PRO A 485 "
        pdb=" CA  PRO A 485 "
        pdb=" C   PRO A 485 "
      ideal   model   delta    sigma   weight residual
     114.68  108.93    5.75 1.28e+00 6.10e-01 2.02e+01
  angle pdb=" C   ASN A 557 "
        pdb=" N   LEU A 558 "
        pdb=" CA  LEU A 558 "
      ideal   model   delta    sigma   weight residual
     121.54  128.71   -7.17 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" C   ASN B 557 "
        pdb=" N   LEU B 558 "
        pdb=" CA  LEU B 558 "
      ideal   model   delta    sigma   weight residual
     121.54  128.67   -7.13 1.91e+00 2.74e-01 1.40e+01
  angle pdb=" C   ASP A 217 "
        pdb=" N   SER A 218 "
        pdb=" CA  SER A 218 "
      ideal   model   delta    sigma   weight residual
     121.54  127.92   -6.38 1.91e+00 2.74e-01 1.12e+01
  ... (remaining 12313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.99: 4745
       16.99 -    33.98: 536
       33.98 -    50.97: 160
       50.97 -    67.96: 48
       67.96 -    84.95: 12
  Dihedral angle restraints: 5501
    sinusoidal: 2241
      harmonic: 3260
  Sorted by residual:
  dihedral pdb=" CB  CYS A 603 "
           pdb=" SG  CYS A 603 "
           pdb=" SG  CYS B 603 "
           pdb=" CB  CYS B 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    8.05   84.95     1      1.00e+01 1.00e-02 8.75e+01
  dihedral pdb=" CA  LEU B 484 "
           pdb=" C   LEU B 484 "
           pdb=" N   PRO B 485 "
           pdb=" CA  PRO B 485 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.76   42.24     0      5.00e+00 4.00e-02 7.14e+01
  dihedral pdb=" CA  LEU A 484 "
           pdb=" C   LEU A 484 "
           pdb=" N   PRO A 485 "
           pdb=" CA  PRO A 485 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.79   42.21     0      5.00e+00 4.00e-02 7.13e+01
  ... (remaining 5498 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1061
       0.058 -    0.116: 308
       0.116 -    0.173: 52
       0.173 -    0.231: 3
       0.231 -    0.289: 3
  Chirality restraints: 1427
  Sorted by residual:
  chirality pdb=" C13 CLR A 701 "
            pdb=" C12 CLR A 701 "
            pdb=" C14 CLR A 701 "
            pdb=" C17 CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.64   -0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" C13 CLR B 702 "
            pdb=" C12 CLR B 702 "
            pdb=" C14 CLR B 702 "
            pdb=" C17 CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.65   -0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" C14 CLR A 701 "
            pdb=" C13 CLR A 701 "
            pdb=" C15 CLR A 701 "
            pdb=" C8  CLR A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.55    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1424 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 484 "   -0.056 5.00e-02 4.00e+02   8.39e-02 1.13e+01
        pdb=" N   PRO A 485 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO A 485 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 485 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 484 "   -0.056 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO B 485 "    0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO B 485 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 485 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 378 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   ARG A 378 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ARG A 378 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TRP A 379 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2348
        2.78 -     3.31: 8136
        3.31 -     3.84: 14661
        3.84 -     4.37: 17074
        4.37 -     4.90: 28878
  Nonbonded interactions: 71097
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 494 "
            pdb=" O   LYS B 500 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OH  TYR A 494 "
            pdb=" O   LYS A 500 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" N   ASN B 338 "
            pdb=" OD1 ASN B 338 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" N   ASN A 338 "
            pdb=" OD1 ASN A 338 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O   LEU A 146 "
            pdb=" OG1 THR A 371 "
     model   vdw
     2.280 3.040
  ... (remaining 71092 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 35 through 654)
  selection = (chain 'B' and resid 35 through 654)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.630
  Find NCS groups from input model:        0.150
  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:   13.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.120   9092  Z= 0.336
  Angle     :  1.017   9.420  12324  Z= 0.548
  Chirality :  0.055   0.289   1427
  Planarity :  0.006   0.084   1522
  Dihedral  : 16.515  83.686   3400
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 10.17 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.74 (0.17), residues: 1116
  helix: -4.22 (0.09), residues: 616
  sheet: -1.30 (0.85), residues: 34
  loop : -3.22 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 137 
 TYR   0.012   0.002   TYR A 613 
 PHE   0.019   0.002   PHE A 489 
 TRP   0.013   0.002   TRP B 627 
 HIS   0.003   0.001   HIS B 375 

Details of bonding type rmsd
  covalent geometry    : bond        0.00706 ( 9089)
  covalent geometry    : angle       1.01654 (12318)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       2.00193 (    6)
  hydrogen bonds       : bond        0.30596 (  365)
  hydrogen bonds       : angle      10.37537 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 325
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 ASN cc_start: 0.7228 (p0) cc_final: 0.6888 (p0)
REVERT: A   86 LYS cc_start: 0.8539 (tttt) cc_final: 0.8250 (ttpt)
REVERT: A  143 SER cc_start: 0.7685 (p) cc_final: 0.7375 (p)
REVERT: A  172 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8627 (ttmt)
REVERT: A  192 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8448 (mmtm)
REVERT: A  240 PHE cc_start: 0.8278 (p90) cc_final: 0.7782 (p90)
REVERT: A  265 MET cc_start: 0.7324 (mmt) cc_final: 0.6997 (tpp)
REVERT: A  266 PHE cc_start: 0.8114 (t80) cc_final: 0.7674 (t80)
REVERT: A  277 PHE cc_start: 0.6539 (m-80) cc_final: 0.6213 (m-80)
REVERT: A  336 TYR cc_start: 0.8117 (t80) cc_final: 0.7728 (t80)
REVERT: A  423 ILE cc_start: 0.9336 (mp) cc_final: 0.9086 (tp)
REVERT: A  430 LEU cc_start: 0.9330 (mt) cc_final: 0.9126 (mt)
REVERT: A  470 PHE cc_start: 0.8828 (t80) cc_final: 0.8621 (t80)
REVERT: A  514 MET cc_start: 0.8620 (ptp) cc_final: 0.8209 (ptt)
REVERT: A  518 TYR cc_start: 0.9095 (m-10) cc_final: 0.8891 (m-80)
REVERT: A  533 VAL cc_start: 0.8838 (m) cc_final: 0.8625 (t)
REVERT: A  548 MET cc_start: 0.8262 (mtt) cc_final: 0.7410 (mtm)
REVERT: A  565 LEU cc_start: 0.9241 (tp) cc_final: 0.9009 (tp)
REVERT: A  573 ILE cc_start: 0.9082 (mt) cc_final: 0.8652 (mt)
REVERT: A  617 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8138 (mm-40)
REVERT: A  629 ASN cc_start: 0.9001 (m-40) cc_final: 0.8615 (m-40)
REVERT: A  652 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8397 (tttt)
REVERT: B   68 ASN cc_start: 0.7211 (p0) cc_final: 0.6828 (p0)
REVERT: B   86 LYS cc_start: 0.8046 (tttt) cc_final: 0.7826 (ttpt)
REVERT: B  137 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7789 (ttm110)
REVERT: B  143 SER cc_start: 0.8117 (p) cc_final: 0.7793 (p)
REVERT: B  198 MET cc_start: 0.9079 (ttm) cc_final: 0.8700 (ttm)
REVERT: B  266 PHE cc_start: 0.8268 (t80) cc_final: 0.7823 (t80)
REVERT: B  277 PHE cc_start: 0.6249 (m-80) cc_final: 0.5995 (m-80)
REVERT: B  336 TYR cc_start: 0.8030 (t80) cc_final: 0.7551 (t80)
REVERT: B  477 ASP cc_start: 0.7927 (t0) cc_final: 0.7632 (t0)
REVERT: B  502 LYS cc_start: 0.8425 (mmtm) cc_final: 0.8165 (ttmt)
REVERT: B  514 MET cc_start: 0.8602 (ptp) cc_final: 0.8053 (ptt)
REVERT: B  523 MET cc_start: 0.8852 (tpt) cc_final: 0.8637 (tpt)
REVERT: B  548 MET cc_start: 0.8375 (mtt) cc_final: 0.7730 (mtm)
REVERT: B  573 ILE cc_start: 0.9234 (mt) cc_final: 0.8765 (mp)
REVERT: B  585 GLU cc_start: 0.8825 (tp30) cc_final: 0.8493 (mm-30)
REVERT: B  605 TYR cc_start: 0.5858 (m-80) cc_final: 0.5302 (m-80)
REVERT: B  629 ASN cc_start: 0.8955 (m-40) cc_final: 0.8475 (m-40)
REVERT: B  630 HIS cc_start: 0.8544 (m170) cc_final: 0.8249 (m170)
REVERT: B  636 MET cc_start: 0.8252 (tpp) cc_final: 0.7997 (tpp)
REVERT: B  646 LEU cc_start: 0.8227 (tt) cc_final: 0.7672 (mm)
REVERT: B  650 PHE cc_start: 0.7850 (m-80) cc_final: 0.7629 (m-10)
  outliers start: 32
  outliers final: 9
  residues processed: 339
  average time/residue: 0.0984
  time to fit residues: 45.0886
Evaluate side-chains
  249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 238
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.1980
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0270
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.8444

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
A  68 ASN
A  76 ASN
A 109 ASN
A 120 ASN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 HIS
A 289 ASN
A 398 GLN
A 425 ASN
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 HIS
A 583 HIS
A 601 ASN
A 629 ASN
A 630 HIS
B  40 HIS
B  76 ASN
B 109 ASN
B 120 ASN
B 289 ASN
B 387 ASN
B 425 ASN
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
B 583 HIS
B 601 ASN
B 629 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.152618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.118388 restraints weight = 16742.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.121105 restraints weight = 10428.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.123002 restraints weight = 7545.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124211 restraints weight = 6064.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124802 restraints weight = 5254.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9092  Z= 0.162
  Angle     :  0.661   6.583  12324  Z= 0.340
  Chirality :  0.041   0.178   1427
  Planarity :  0.005   0.069   1522
  Dihedral  :  7.014  54.387   1382
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.08 %
    Favored  : 94.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.88 (0.21), residues: 1116
  helix: -2.18 (0.17), residues: 630
  sheet: -1.35 (0.73), residues: 34
  loop : -3.14 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 191 
 TYR   0.014   0.001   TYR B 494 
 PHE   0.019   0.002   PHE B 489 
 TRP   0.006   0.001   TRP B 379 
 HIS   0.008   0.001   HIS A 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9089)
  covalent geometry    : angle       0.66116 (12318)
  SS BOND              : bond        0.00283 (    3)
  SS BOND              : angle       1.02067 (    6)
  hydrogen bonds       : bond        0.04373 (  365)
  hydrogen bonds       : angle       5.23848 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 299
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LYS cc_start: 0.8436 (tttt) cc_final: 0.8168 (ttpt)
REVERT: A  131 MET cc_start: 0.8183 (mmm) cc_final: 0.7976 (mmm)
REVERT: A  143 SER cc_start: 0.7643 (p) cc_final: 0.7315 (p)
REVERT: A  192 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8667 (mmmm)
REVERT: A  196 ILE cc_start: 0.8989 (mt) cc_final: 0.8735 (mm)
REVERT: A  240 PHE cc_start: 0.8736 (p90) cc_final: 0.8125 (p90)
REVERT: A  266 PHE cc_start: 0.8264 (t80) cc_final: 0.7791 (t80)
REVERT: A  277 PHE cc_start: 0.6448 (m-80) cc_final: 0.5994 (m-80)
REVERT: A  336 TYR cc_start: 0.8020 (t80) cc_final: 0.7721 (t80)
REVERT: A  470 PHE cc_start: 0.8768 (t80) cc_final: 0.8506 (t80)
REVERT: A  514 MET cc_start: 0.8525 (ptp) cc_final: 0.8056 (ptt)
REVERT: A  557 ASN cc_start: 0.8127 (t0) cc_final: 0.7475 (m-40)
REVERT: A  565 LEU cc_start: 0.9051 (tp) cc_final: 0.8835 (tp)
REVERT: A  617 GLN cc_start: 0.8823 (mm-40) cc_final: 0.7973 (mm-40)
REVERT: A  629 ASN cc_start: 0.8999 (m110) cc_final: 0.8667 (m-40)
REVERT: A  652 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8523 (tttt)
REVERT: B   71 MET cc_start: 0.7882 (mmm) cc_final: 0.7118 (mmm)
REVERT: B  105 ASP cc_start: 0.7941 (t70) cc_final: 0.7715 (t0)
REVERT: B  143 SER cc_start: 0.8136 (p) cc_final: 0.7834 (p)
REVERT: B  160 ARG cc_start: 0.8505 (ttm110) cc_final: 0.7699 (tpt170)
REVERT: B  198 MET cc_start: 0.9111 (ttm) cc_final: 0.8588 (ttm)
REVERT: B  253 PHE cc_start: 0.7546 (m-80) cc_final: 0.7282 (m-80)
REVERT: B  477 ASP cc_start: 0.8099 (t0) cc_final: 0.7875 (t0)
REVERT: B  514 MET cc_start: 0.8596 (ptp) cc_final: 0.8083 (ptt)
REVERT: B  548 MET cc_start: 0.8058 (mtt) cc_final: 0.7770 (mtt)
REVERT: B  585 GLU cc_start: 0.8618 (tp30) cc_final: 0.8384 (mm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 301
  average time/residue: 0.0815
  time to fit residues: 35.0813
Evaluate side-chains
  230 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 80 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 102 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 283 HIS
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.149616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116581 restraints weight = 16490.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.119313 restraints weight = 10099.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121183 restraints weight = 7195.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.122395 restraints weight = 5723.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.123014 restraints weight = 4919.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9092  Z= 0.171
  Angle     :  0.649  11.034  12324  Z= 0.329
  Chirality :  0.041   0.139   1427
  Planarity :  0.004   0.071   1522
  Dihedral  :  6.857  47.308   1382
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.23), residues: 1116
  helix: -1.18 (0.19), residues: 608
  sheet: -1.27 (0.77), residues: 34
  loop : -3.12 (0.26), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 236 
 TYR   0.016   0.002   TYR A 494 
 PHE   0.024   0.002   PHE B 506 
 TRP   0.007   0.001   TRP A 379 
 HIS   0.009   0.002   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 9089)
  covalent geometry    : angle       0.64863 (12318)
  SS BOND              : bond        0.01862 (    3)
  SS BOND              : angle       1.08620 (    6)
  hydrogen bonds       : bond        0.03768 (  365)
  hydrogen bonds       : angle       4.81040 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7882 (mmt) cc_final: 0.7383 (mmm)
REVERT: A   81 PRO cc_start: 0.8454 (Cg_endo) cc_final: 0.7898 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8482 (tttt) cc_final: 0.8204 (ttpt)
REVERT: A  131 MET cc_start: 0.8314 (mmm) cc_final: 0.7939 (mmm)
REVERT: A  143 SER cc_start: 0.7833 (p) cc_final: 0.7592 (p)
REVERT: A  192 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8539 (mmmm)
REVERT: A  240 PHE cc_start: 0.8694 (p90) cc_final: 0.8263 (p90)
REVERT: A  277 PHE cc_start: 0.6473 (m-80) cc_final: 0.5951 (m-80)
REVERT: A  458 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7580 (mm-30)
REVERT: A  470 PHE cc_start: 0.8788 (t80) cc_final: 0.8540 (t80)
REVERT: A  557 ASN cc_start: 0.8239 (t0) cc_final: 0.7760 (m-40)
REVERT: A  565 LEU cc_start: 0.9074 (tp) cc_final: 0.8845 (tp)
REVERT: A  617 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8000 (mm-40)
REVERT: A  629 ASN cc_start: 0.8998 (m110) cc_final: 0.8609 (m-40)
REVERT: A  652 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8442 (tttt)
REVERT: B   71 MET cc_start: 0.7849 (mmm) cc_final: 0.6958 (mmm)
REVERT: B   81 PRO cc_start: 0.7960 (Cg_endo) cc_final: 0.7723 (Cg_exo)
REVERT: B   96 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7228 (mmm-85)
REVERT: B  143 SER cc_start: 0.8195 (p) cc_final: 0.7922 (p)
REVERT: B  160 ARG cc_start: 0.8771 (ttm110) cc_final: 0.7916 (tpt170)
REVERT: B  277 PHE cc_start: 0.6531 (m-80) cc_final: 0.6013 (m-80)
REVERT: B  424 GLN cc_start: 0.6877 (tt0) cc_final: 0.6636 (mt0)
REVERT: B  430 LEU cc_start: 0.9485 (mt) cc_final: 0.9258 (mt)
REVERT: B  460 ILE cc_start: 0.9069 (tp) cc_final: 0.8699 (tp)
REVERT: B  585 GLU cc_start: 0.8678 (tp30) cc_final: 0.8430 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 292
  average time/residue: 0.0774
  time to fit residues: 32.8107
Evaluate side-chains
  233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 HIS
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
B 141 GLN
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.153442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118380 restraints weight = 16788.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.121422 restraints weight = 9932.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.123649 restraints weight = 6958.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.125065 restraints weight = 5442.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.125863 restraints weight = 4628.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9092  Z= 0.125
  Angle     :  0.614   9.112  12324  Z= 0.304
  Chirality :  0.040   0.140   1427
  Planarity :  0.004   0.074   1522
  Dihedral  :  6.235  41.730   1382
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.57 (0.24), residues: 1116
  helix: -0.84 (0.20), residues: 612
  sheet: -1.09 (0.79), residues: 34
  loop : -2.95 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 163 
 TYR   0.016   0.001   TYR A 464 
 PHE   0.023   0.002   PHE B 385 
 TRP   0.007   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9089)
  covalent geometry    : angle       0.61380 (12318)
  SS BOND              : bond        0.00381 (    3)
  SS BOND              : angle       1.34978 (    6)
  hydrogen bonds       : bond        0.03232 (  365)
  hydrogen bonds       : angle       4.68444 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7870 (mmt) cc_final: 0.7432 (mmm)
REVERT: A   81 PRO cc_start: 0.8319 (Cg_endo) cc_final: 0.7870 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8417 (tttt) cc_final: 0.8149 (ttpt)
REVERT: A  131 MET cc_start: 0.8388 (mmm) cc_final: 0.8051 (mmm)
REVERT: A  141 GLN cc_start: 0.8122 (mp-120) cc_final: 0.7839 (mp10)
REVERT: A  192 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8559 (mmmm)
REVERT: A  240 PHE cc_start: 0.8586 (p90) cc_final: 0.8168 (p90)
REVERT: A  277 PHE cc_start: 0.6353 (m-80) cc_final: 0.5880 (m-80)
REVERT: A  384 SER cc_start: 0.9200 (t) cc_final: 0.8984 (t)
REVERT: A  458 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7436 (mm-30)
REVERT: A  514 MET cc_start: 0.7740 (ptp) cc_final: 0.7505 (ptt)
REVERT: A  557 ASN cc_start: 0.8213 (t0) cc_final: 0.7842 (m-40)
REVERT: A  565 LEU cc_start: 0.8970 (tp) cc_final: 0.8728 (tp)
REVERT: A  617 GLN cc_start: 0.8459 (mm-40) cc_final: 0.7801 (mm-40)
REVERT: A  629 ASN cc_start: 0.8849 (m110) cc_final: 0.8370 (m-40)
REVERT: B   71 MET cc_start: 0.7747 (mmm) cc_final: 0.7068 (mmm)
REVERT: B   81 PRO cc_start: 0.7852 (Cg_endo) cc_final: 0.7648 (Cg_exo)
REVERT: B   96 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7259 (mmm-85)
REVERT: B  143 SER cc_start: 0.8084 (p) cc_final: 0.7842 (p)
REVERT: B  160 ARG cc_start: 0.8682 (ttm110) cc_final: 0.7865 (tpt170)
REVERT: B  238 ILE cc_start: 0.9281 (mp) cc_final: 0.9063 (mp)
REVERT: B  277 PHE cc_start: 0.6218 (m-80) cc_final: 0.5963 (m-80)
REVERT: B  342 TYR cc_start: 0.7273 (t80) cc_final: 0.6926 (t80)
REVERT: B  424 GLN cc_start: 0.6738 (tt0) cc_final: 0.6480 (mt0)
REVERT: B  430 LEU cc_start: 0.9350 (mt) cc_final: 0.9117 (mt)
REVERT: B  460 ILE cc_start: 0.9103 (tp) cc_final: 0.8740 (tp)
REVERT: B  581 LEU cc_start: 0.9556 (mp) cc_final: 0.9348 (mp)
REVERT: B  585 GLU cc_start: 0.8566 (tp30) cc_final: 0.8290 (mm-30)
REVERT: B  604 ASN cc_start: 0.7367 (p0) cc_final: 0.7107 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.0830
  time to fit residues: 36.3409
Evaluate side-chains
  240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0270
   chunk 97 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0570
   chunk 93 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 HIS
A 391 ASN
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 457 HIS
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.155863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.122054 restraints weight = 16761.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.124773 restraints weight = 10498.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.126670 restraints weight = 7621.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.127641 restraints weight = 6158.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128610 restraints weight = 5392.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9092  Z= 0.108
  Angle     :  0.598   6.695  12324  Z= 0.295
  Chirality :  0.040   0.138   1427
  Planarity :  0.004   0.074   1522
  Dihedral  :  5.799  38.780   1382
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.24), residues: 1116
  helix: -0.62 (0.20), residues: 616
  sheet: -0.85 (0.73), residues: 34
  loop : -2.71 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 163 
 TYR   0.018   0.001   TYR A 494 
 PHE   0.023   0.002   PHE B 385 
 TRP   0.006   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9089)
  covalent geometry    : angle       0.59758 (12318)
  SS BOND              : bond        0.00598 (    3)
  SS BOND              : angle       1.36317 (    6)
  hydrogen bonds       : bond        0.02956 (  365)
  hydrogen bonds       : angle       4.48159 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 300
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.7951 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8478 (tttt) cc_final: 0.8250 (ttpt)
REVERT: A  117 PHE cc_start: 0.8699 (t80) cc_final: 0.8411 (t80)
REVERT: A  120 ASN cc_start: 0.8149 (p0) cc_final: 0.7394 (m110)
REVERT: A  131 MET cc_start: 0.8227 (mmm) cc_final: 0.7930 (mmm)
REVERT: A  134 LEU cc_start: 0.7656 (mp) cc_final: 0.7341 (tp)
REVERT: A  141 GLN cc_start: 0.8333 (mp-120) cc_final: 0.7950 (mp10)
REVERT: A  192 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8731 (mmmm)
REVERT: A  240 PHE cc_start: 0.8573 (p90) cc_final: 0.8210 (p90)
REVERT: A  277 PHE cc_start: 0.6509 (m-80) cc_final: 0.6075 (m-80)
REVERT: A  384 SER cc_start: 0.9234 (t) cc_final: 0.8897 (t)
REVERT: A  458 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7302 (mm-30)
REVERT: A  514 MET cc_start: 0.7976 (ptp) cc_final: 0.7652 (ptt)
REVERT: A  557 ASN cc_start: 0.8253 (t0) cc_final: 0.7871 (m-40)
REVERT: A  565 LEU cc_start: 0.9054 (tp) cc_final: 0.8822 (tp)
REVERT: A  617 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7846 (mm-40)
REVERT: A  629 ASN cc_start: 0.8862 (m110) cc_final: 0.8484 (m-40)
REVERT: B   71 MET cc_start: 0.7681 (mmm) cc_final: 0.6933 (mmm)
REVERT: B   96 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7352 (mmm-85)
REVERT: B  152 MET cc_start: 0.6627 (ptp) cc_final: 0.6379 (ptp)
REVERT: B  160 ARG cc_start: 0.8897 (ttm110) cc_final: 0.7894 (tpt-90)
REVERT: B  187 SER cc_start: 0.8344 (m) cc_final: 0.7905 (p)
REVERT: B  238 ILE cc_start: 0.9200 (mp) cc_final: 0.8982 (mp)
REVERT: B  277 PHE cc_start: 0.6428 (m-80) cc_final: 0.6021 (m-80)
REVERT: B  342 TYR cc_start: 0.7432 (t80) cc_final: 0.7110 (t80)
REVERT: B  514 MET cc_start: 0.7908 (ptp) cc_final: 0.7584 (ptt)
REVERT: B  581 LEU cc_start: 0.9549 (mp) cc_final: 0.9344 (mp)
REVERT: B  585 GLU cc_start: 0.8779 (tp30) cc_final: 0.8477 (mm-30)
REVERT: B  604 ASN cc_start: 0.7229 (p0) cc_final: 0.6996 (p0)
REVERT: B  629 ASN cc_start: 0.8972 (m110) cc_final: 0.8450 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 300
  average time/residue: 0.0847
  time to fit residues: 36.4464
Evaluate side-chains
  234 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 93 optimal weight:    0.9980
   chunk 104 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 109 optimal weight:    1.9990
   chunk 82 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 81 optimal weight:   30.0000
   chunk 94 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
A  76 ASN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 HIS
A 437 GLN
A 630 HIS
B  41 ASN
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.155870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122230 restraints weight = 16827.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124995 restraints weight = 10558.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.126957 restraints weight = 7609.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.128270 restraints weight = 6101.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.128934 restraints weight = 5260.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9092  Z= 0.120
  Angle     :  0.620   8.102  12324  Z= 0.303
  Chirality :  0.041   0.181   1427
  Planarity :  0.004   0.074   1522
  Dihedral  :  5.654  39.867   1382
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.25), residues: 1116
  helix: -0.29 (0.21), residues: 586
  sheet: -0.73 (0.75), residues: 34
  loop : -2.65 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  96 
 TYR   0.014   0.001   TYR A 494 
 PHE   0.029   0.002   PHE A 511 
 TRP   0.007   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9089)
  covalent geometry    : angle       0.61972 (12318)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       1.03515 (    6)
  hydrogen bonds       : bond        0.02983 (  365)
  hydrogen bonds       : angle       4.47212 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7751 (mmt) cc_final: 0.7133 (mmm)
REVERT: A   81 PRO cc_start: 0.8327 (Cg_endo) cc_final: 0.7953 (Cg_exo)
REVERT: A  105 ASP cc_start: 0.7215 (t0) cc_final: 0.6912 (t0)
REVERT: A  117 PHE cc_start: 0.8679 (t80) cc_final: 0.8411 (t80)
REVERT: A  120 ASN cc_start: 0.8125 (p0) cc_final: 0.7405 (m110)
REVERT: A  131 MET cc_start: 0.8325 (mmm) cc_final: 0.8015 (mmm)
REVERT: A  134 LEU cc_start: 0.7583 (mp) cc_final: 0.7075 (tt)
REVERT: A  192 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8763 (mmmm)
REVERT: A  238 ILE cc_start: 0.9015 (mp) cc_final: 0.8697 (mp)
REVERT: A  240 PHE cc_start: 0.8643 (p90) cc_final: 0.8217 (p90)
REVERT: A  277 PHE cc_start: 0.6399 (m-80) cc_final: 0.5960 (m-80)
REVERT: A  384 SER cc_start: 0.9129 (t) cc_final: 0.8890 (t)
REVERT: A  458 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: A  514 MET cc_start: 0.7993 (ptp) cc_final: 0.7614 (ptt)
REVERT: A  565 LEU cc_start: 0.9100 (tp) cc_final: 0.8863 (tp)
REVERT: A  617 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8398 (mm-40)
REVERT: A  629 ASN cc_start: 0.8852 (m110) cc_final: 0.8292 (m-40)
REVERT: B   71 MET cc_start: 0.7674 (mmm) cc_final: 0.6902 (mmm)
REVERT: B   96 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7329 (mmm-85)
REVERT: B  160 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8079 (tpt-90)
REVERT: B  187 SER cc_start: 0.8314 (m) cc_final: 0.7850 (p)
REVERT: B  277 PHE cc_start: 0.6276 (m-80) cc_final: 0.6064 (m-80)
REVERT: B  342 TYR cc_start: 0.7369 (t80) cc_final: 0.7077 (t80)
REVERT: B  442 VAL cc_start: 0.8418 (t) cc_final: 0.8147 (m)
REVERT: B  514 MET cc_start: 0.8050 (ptp) cc_final: 0.7660 (ptt)
REVERT: B  541 MET cc_start: 0.8835 (tmm) cc_final: 0.8553 (tmm)
REVERT: B  604 ASN cc_start: 0.7243 (p0) cc_final: 0.6995 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.0797
  time to fit residues: 32.9885
Evaluate side-chains
  231 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 88 optimal weight:    0.0070
   chunk 77 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 582 GLN
A 630 HIS
B 222 ASN
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.156624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.126308 restraints weight = 16939.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.127036 restraints weight = 12473.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.127408 restraints weight = 9187.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.127544 restraints weight = 8338.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.129243 restraints weight = 7793.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9092  Z= 0.117
  Angle     :  0.627   8.474  12324  Z= 0.306
  Chirality :  0.041   0.158   1427
  Planarity :  0.004   0.073   1522
  Dihedral  :  5.582  40.516   1382
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.25), residues: 1116
  helix: -0.12 (0.21), residues: 588
  sheet: -0.45 (0.80), residues: 34
  loop : -2.68 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 163 
 TYR   0.015   0.001   TYR B 464 
 PHE   0.022   0.001   PHE B 489 
 TRP   0.009   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9089)
  covalent geometry    : angle       0.62706 (12318)
  SS BOND              : bond        0.00336 (    3)
  SS BOND              : angle       1.12226 (    6)
  hydrogen bonds       : bond        0.02972 (  365)
  hydrogen bonds       : angle       4.37235 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7666 (mmt) cc_final: 0.7418 (mmm)
REVERT: A   72 LYS cc_start: 0.7913 (tttp) cc_final: 0.7671 (ttmm)
REVERT: A  120 ASN cc_start: 0.7978 (p0) cc_final: 0.7301 (m110)
REVERT: A  131 MET cc_start: 0.8253 (mmm) cc_final: 0.7924 (mmm)
REVERT: A  134 LEU cc_start: 0.7635 (mp) cc_final: 0.7325 (tp)
REVERT: A  192 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8761 (mmmm)
REVERT: A  199 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7186 (mm-30)
REVERT: A  238 ILE cc_start: 0.9022 (mp) cc_final: 0.8669 (mp)
REVERT: A  240 PHE cc_start: 0.8670 (p90) cc_final: 0.8219 (p90)
REVERT: A  277 PHE cc_start: 0.6349 (m-80) cc_final: 0.5936 (m-80)
REVERT: A  384 SER cc_start: 0.9227 (t) cc_final: 0.8961 (t)
REVERT: A  455 PHE cc_start: 0.8299 (t80) cc_final: 0.8067 (t80)
REVERT: A  458 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7293 (mm-30)
REVERT: A  514 MET cc_start: 0.7736 (ptp) cc_final: 0.7469 (ptt)
REVERT: A  541 MET cc_start: 0.8748 (tmm) cc_final: 0.8488 (tmm)
REVERT: A  549 MET cc_start: 0.8318 (ttt) cc_final: 0.7929 (tmm)
REVERT: A  565 LEU cc_start: 0.9043 (tp) cc_final: 0.8797 (tp)
REVERT: A  629 ASN cc_start: 0.8810 (m110) cc_final: 0.8444 (m-40)
REVERT: B   71 MET cc_start: 0.7554 (mmm) cc_final: 0.6843 (mmm)
REVERT: B  160 ARG cc_start: 0.8829 (ttm110) cc_final: 0.7927 (tpt-90)
REVERT: B  187 SER cc_start: 0.8501 (m) cc_final: 0.8047 (p)
REVERT: B  238 ILE cc_start: 0.9190 (mp) cc_final: 0.8960 (mp)
REVERT: B  277 PHE cc_start: 0.6450 (m-80) cc_final: 0.6123 (m-80)
REVERT: B  342 TYR cc_start: 0.7307 (t80) cc_final: 0.7009 (t80)
REVERT: B  514 MET cc_start: 0.7978 (ptp) cc_final: 0.7560 (ptt)
REVERT: B  604 ASN cc_start: 0.7302 (p0) cc_final: 0.7028 (p0)
REVERT: B  629 ASN cc_start: 0.8958 (m110) cc_final: 0.8385 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 284
  average time/residue: 0.0790
  time to fit residues: 32.4586
Evaluate side-chains
  233 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 398 GLN
A 630 HIS
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.153103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.118486 restraints weight = 16733.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.121455 restraints weight = 10076.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.123469 restraints weight = 7102.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.124815 restraints weight = 5614.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.125485 restraints weight = 4822.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9092  Z= 0.156
  Angle     :  0.663   9.710  12324  Z= 0.325
  Chirality :  0.042   0.156   1427
  Planarity :  0.004   0.073   1522
  Dihedral  :  5.810  41.418   1382
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.86 (0.25), residues: 1116
  helix: -0.18 (0.21), residues: 590
  sheet: -0.50 (0.85), residues: 34
  loop : -2.67 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.019   0.002   TYR B 464 
 PHE   0.032   0.002   PHE A 511 
 TRP   0.008   0.001   TRP B 379 
 HIS   0.004   0.001   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 9089)
  covalent geometry    : angle       0.66238 (12318)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       1.03556 (    6)
  hydrogen bonds       : bond        0.03245 (  365)
  hydrogen bonds       : angle       4.52813 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 276
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7742 (mmt) cc_final: 0.7420 (mmm)
REVERT: A  105 ASP cc_start: 0.7151 (t0) cc_final: 0.6910 (t0)
REVERT: A  119 CYS cc_start: 0.7243 (t) cc_final: 0.6938 (t)
REVERT: A  120 ASN cc_start: 0.7892 (p0) cc_final: 0.7295 (m-40)
REVERT: A  131 MET cc_start: 0.8335 (mmm) cc_final: 0.7987 (mmm)
REVERT: A  160 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8306 (ttp-110)
REVERT: A  192 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8755 (mmmm)
REVERT: A  199 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6787 (mm-30)
REVERT: A  240 PHE cc_start: 0.8832 (p90) cc_final: 0.8384 (p90)
REVERT: A  265 MET cc_start: 0.7683 (mmp) cc_final: 0.7211 (mmm)
REVERT: A  277 PHE cc_start: 0.6570 (m-80) cc_final: 0.6077 (m-80)
REVERT: A  346 LYS cc_start: 0.7401 (tptp) cc_final: 0.7157 (mtpp)
REVERT: A  384 SER cc_start: 0.9192 (t) cc_final: 0.8944 (t)
REVERT: A  458 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: A  514 MET cc_start: 0.7788 (ptp) cc_final: 0.7506 (ptt)
REVERT: A  565 LEU cc_start: 0.9074 (tp) cc_final: 0.8850 (tp)
REVERT: A  629 ASN cc_start: 0.8790 (m110) cc_final: 0.8303 (m-40)
REVERT: B   71 MET cc_start: 0.7642 (mmm) cc_final: 0.6844 (mmm)
REVERT: B  160 ARG cc_start: 0.8694 (ttm110) cc_final: 0.7774 (tpt-90)
REVERT: B  187 SER cc_start: 0.8048 (m) cc_final: 0.7720 (p)
REVERT: B  238 ILE cc_start: 0.9190 (mp) cc_final: 0.8965 (mp)
REVERT: B  277 PHE cc_start: 0.6323 (m-80) cc_final: 0.6080 (m-80)
REVERT: B  342 TYR cc_start: 0.7234 (t80) cc_final: 0.6983 (t80)
REVERT: B  442 VAL cc_start: 0.8565 (t) cc_final: 0.8329 (t)
REVERT: B  514 MET cc_start: 0.7984 (ptp) cc_final: 0.7629 (ptt)
REVERT: B  541 MET cc_start: 0.8644 (tmm) cc_final: 0.8394 (tmm)
REVERT: B  604 ASN cc_start: 0.7397 (p0) cc_final: 0.7079 (p0)
REVERT: B  629 ASN cc_start: 0.8963 (m110) cc_final: 0.8432 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 276
  average time/residue: 0.0773
  time to fit residues: 31.1947
Evaluate side-chains
  234 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 630 HIS
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.145118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.114414 restraints weight = 16993.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115036 restraints weight = 11370.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.115909 restraints weight = 7611.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.116300 restraints weight = 6918.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.116484 restraints weight = 6310.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9092  Z= 0.270
  Angle     :  0.780  10.213  12324  Z= 0.394
  Chirality :  0.047   0.177   1427
  Planarity :  0.005   0.066   1522
  Dihedral  :  6.811  44.399   1382
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.13 (0.25), residues: 1116
  helix: -0.35 (0.21), residues: 586
  sheet: -1.43 (0.73), residues: 46
  loop : -2.82 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 193 
 TYR   0.023   0.003   TYR A 342 
 PHE   0.031   0.003   PHE A 545 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.005   0.001   HIS B 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9089)
  covalent geometry    : angle       0.77972 (12318)
  SS BOND              : bond        0.00488 (    3)
  SS BOND              : angle       0.97949 (    6)
  hydrogen bonds       : bond        0.04105 (  365)
  hydrogen bonds       : angle       4.98220 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7781 (mmt) cc_final: 0.7466 (mmm)
REVERT: A  105 ASP cc_start: 0.7431 (t0) cc_final: 0.7124 (t0)
REVERT: A  117 PHE cc_start: 0.8905 (t80) cc_final: 0.8638 (t80)
REVERT: A  120 ASN cc_start: 0.7938 (p0) cc_final: 0.7451 (m-40)
REVERT: A  131 MET cc_start: 0.8263 (mmm) cc_final: 0.7820 (mmm)
REVERT: A  192 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8767 (mmmm)
REVERT: A  199 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7042 (mm-30)
REVERT: A  240 PHE cc_start: 0.8925 (p90) cc_final: 0.8525 (p90)
REVERT: A  265 MET cc_start: 0.7935 (mmp) cc_final: 0.7501 (mmm)
REVERT: A  277 PHE cc_start: 0.6897 (m-80) cc_final: 0.6203 (m-80)
REVERT: A  342 TYR cc_start: 0.7046 (t80) cc_final: 0.6541 (t80)
REVERT: A  346 LYS cc_start: 0.7925 (tptp) cc_final: 0.7623 (mtpp)
REVERT: A  430 LEU cc_start: 0.9479 (mt) cc_final: 0.9271 (mt)
REVERT: A  458 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7565 (mm-30)
REVERT: A  470 PHE cc_start: 0.8913 (t80) cc_final: 0.8619 (t80)
REVERT: A  490 THR cc_start: 0.8568 (p) cc_final: 0.8059 (p)
REVERT: A  514 MET cc_start: 0.8146 (ptp) cc_final: 0.7749 (ptt)
REVERT: A  629 ASN cc_start: 0.8907 (m110) cc_final: 0.8393 (m-40)
REVERT: B   71 MET cc_start: 0.7716 (mmm) cc_final: 0.6853 (mmm)
REVERT: B  160 ARG cc_start: 0.8907 (ttm110) cc_final: 0.8551 (ttp-110)
REVERT: B  199 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6663 (mm-30)
REVERT: B  342 TYR cc_start: 0.7468 (t80) cc_final: 0.7119 (t80)
REVERT: B  604 ASN cc_start: 0.7811 (p0) cc_final: 0.7454 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.0808
  time to fit residues: 31.0444
Evaluate side-chains
  228 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 107 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9980
   chunk 111 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.152844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119000 restraints weight = 16751.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121619 restraints weight = 10741.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.123490 restraints weight = 7859.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.124517 restraints weight = 6339.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.125439 restraints weight = 5548.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9092  Z= 0.122
  Angle     :  0.664   9.671  12324  Z= 0.325
  Chirality :  0.042   0.194   1427
  Planarity :  0.004   0.066   1522
  Dihedral  :  6.019  45.775   1382
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.25), residues: 1116
  helix: -0.33 (0.21), residues: 600
  sheet: -0.87 (0.85), residues: 34
  loop : -2.62 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 263 
 TYR   0.028   0.001   TYR A 342 
 PHE   0.039   0.002   PHE B 545 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9089)
  covalent geometry    : angle       0.66411 (12318)
  SS BOND              : bond        0.00310 (    3)
  SS BOND              : angle       0.98958 (    6)
  hydrogen bonds       : bond        0.03422 (  365)
  hydrogen bonds       : angle       4.57179 ( 1059)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7868 (mmt) cc_final: 0.7552 (mmm)
REVERT: A  105 ASP cc_start: 0.7174 (t0) cc_final: 0.6907 (t0)
REVERT: A  119 CYS cc_start: 0.7302 (t) cc_final: 0.6894 (t)
REVERT: A  120 ASN cc_start: 0.7749 (p0) cc_final: 0.7139 (m-40)
REVERT: A  131 MET cc_start: 0.8208 (mmm) cc_final: 0.7823 (mmm)
REVERT: A  192 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8743 (mmmm)
REVERT: A  199 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6787 (mm-30)
REVERT: A  240 PHE cc_start: 0.8829 (p90) cc_final: 0.8364 (p90)
REVERT: A  259 LEU cc_start: 0.8390 (mp) cc_final: 0.8000 (mt)
REVERT: A  265 MET cc_start: 0.7672 (mmp) cc_final: 0.7077 (mmm)
REVERT: A  277 PHE cc_start: 0.6727 (m-80) cc_final: 0.6066 (m-80)
REVERT: A  342 TYR cc_start: 0.7025 (t80) cc_final: 0.6533 (t80)
REVERT: A  346 LYS cc_start: 0.7831 (tptp) cc_final: 0.7565 (mtpp)
REVERT: A  384 SER cc_start: 0.9346 (t) cc_final: 0.9108 (t)
REVERT: A  423 ILE cc_start: 0.9089 (tp) cc_final: 0.8696 (mt)
REVERT: A  458 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7579 (mm-30)
REVERT: A  483 MET cc_start: 0.8454 (ttp) cc_final: 0.8221 (ttm)
REVERT: A  514 MET cc_start: 0.7965 (ptp) cc_final: 0.7637 (ptt)
REVERT: A  604 ASN cc_start: 0.7899 (p0) cc_final: 0.7695 (p0)
REVERT: B   71 MET cc_start: 0.7643 (mmm) cc_final: 0.6825 (mmm)
REVERT: B  160 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8615 (ttp-110)
REVERT: B  199 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6629 (mm-30)
REVERT: B  233 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8317 (mtmt)
REVERT: B  238 ILE cc_start: 0.9198 (mp) cc_final: 0.8968 (mp)
REVERT: B  276 TYR cc_start: 0.7867 (t80) cc_final: 0.7076 (t80)
REVERT: B  342 TYR cc_start: 0.7388 (t80) cc_final: 0.7158 (t80)
REVERT: B  458 GLU cc_start: 0.7643 (tp30) cc_final: 0.7398 (tp30)
REVERT: B  490 THR cc_start: 0.8416 (p) cc_final: 0.8190 (p)
REVERT: B  514 MET cc_start: 0.8076 (ptp) cc_final: 0.7593 (ptt)
REVERT: B  581 LEU cc_start: 0.9569 (mp) cc_final: 0.9368 (mt)
REVERT: B  604 ASN cc_start: 0.7678 (p0) cc_final: 0.7378 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.0844
  time to fit residues: 33.3169
Evaluate side-chains
  237 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 93 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
B  68 ASN
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.154240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119935 restraints weight = 16916.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122816 restraints weight = 10292.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.124892 restraints weight = 7315.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.126136 restraints weight = 5803.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.127150 restraints weight = 4987.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9092  Z= 0.118
  Angle     :  0.655   8.224  12324  Z= 0.323
  Chirality :  0.042   0.201   1427
  Planarity :  0.004   0.068   1522
  Dihedral  :  5.736  46.446   1382
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.41 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.25), residues: 1116
  helix: -0.26 (0.21), residues: 612
  sheet: -0.80 (0.81), residues: 34
  loop : -2.57 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 147 
 TYR   0.027   0.001   TYR A 342 
 PHE   0.035   0.002   PHE B 511 
 TRP   0.011   0.001   TRP B 379 
 HIS   0.004   0.001   HIS B 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9089)
  covalent geometry    : angle       0.65476 (12318)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       1.08782 (    6)
  hydrogen bonds       : bond        0.03405 (  365)
  hydrogen bonds       : angle       4.57394 ( 1059)

===============================================================================
Job complete
usr+sys time: 1543.97 seconds
wall clock time: 27 minutes 27.94 seconds (1647.94 seconds total)