Starting phenix.real_space_refine
on Sun Jul 27 04:12:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_21440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_21440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_21440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_21440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxj_21440/07_2025/6vxj_21440.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.14, per 1000 atoms: 0.69
  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: 2.30
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.92
  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: 2.75

  Time building geometry restraints manager: 2.71 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:             0.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.520
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.370
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.013   0.002   TRP B 627 
 HIS   0.003   0.001   HIS B 375 
 PHE   0.019   0.002   PHE A 489 
 TYR   0.012   0.002   TYR A 613 
 ARG   0.002   0.001   ARG B 137 

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

*********************** 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  : 1.074 
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: 0.8829 (t80) cc_final: 0.8620 (t80)
REVERT: A  514 MET cc_start: 0.8620 (ptp) cc_final: 0.8208 (ptt)
REVERT: A  518 TYR cc_start: 0.9095 (m-10) cc_final: 0.8891 (m-80)
REVERT: A  533 VAL cc_start: 0.8837 (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: 0.7210 (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: 0.7926 (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: 0.8374 (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: 0.8824 (tp30) cc_final: 0.8493 (mm-30)
REVERT: B  605 TYR cc_start: 0.5857 (m-80) cc_final: 0.5301 (m-80)
REVERT: B  629 ASN cc_start: 0.8956 (m-40) cc_final: 0.8474 (m-40)
REVERT: B  630 HIS cc_start: 0.8543 (m170) cc_final: 0.8249 (m170)
REVERT: B  636 MET cc_start: 0.8253 (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: 0.2278
  time to fit residues: 104.0993
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  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 57 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0470
   chunk 65 optimal weight:    9.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7080

-------------------------------------------------------------------------------
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 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 583 HIS
A 601 ASN
A 629 ASN
A 630 HIS
B  40 HIS
B  76 ASN
B 109 ASN
B 141 GLN
B 289 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: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.155370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121369 restraints weight = 16508.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.124129 restraints weight = 10249.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.126047 restraints weight = 7404.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2528

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= 0.129
  Angle     :  0.645   7.072  12324  Z= 0.328
  Chirality :  0.041   0.174   1427
  Planarity :  0.005   0.078   1522
  Dihedral  :  7.005  54.308   1382
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.36 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.21), residues: 1116
  helix: -2.24 (0.17), residues: 632
  sheet: -1.11 (0.74), residues: 34
  loop : -3.18 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 379 
 HIS   0.009   0.001   HIS A 283 
 PHE   0.019   0.002   PHE B 489 
 TYR   0.012   0.001   TYR A 459 
 ARG   0.003   0.000   ARG A 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  365)
  hydrogen bonds       : angle       5.23066 ( 1059)
  SS BOND              : bond        0.00373 (    3)
  SS BOND              : angle       1.08294 (    6)
  covalent geometry    : bond        0.00292 ( 9089)
  covalent geometry    : angle       0.64459 (12318)

*********************** 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
  317 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 314
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LYS cc_start: 0.8376 (tttt) cc_final: 0.7989 (ttpt)
REVERT: A  137 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7800 (ttm110)
REVERT: A  143 SER cc_start: 0.7635 (p) cc_final: 0.7379 (p)
REVERT: A  192 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8513 (mmmm)
REVERT: A  240 PHE cc_start: 0.8611 (p90) cc_final: 0.7961 (p90)
REVERT: A  266 PHE cc_start: 0.8140 (t80) cc_final: 0.7798 (t80)
REVERT: A  336 TYR cc_start: 0.7920 (t80) cc_final: 0.7685 (t80)
REVERT: A  470 PHE cc_start: 0.8710 (t80) cc_final: 0.8167 (t80)
REVERT: A  514 MET cc_start: 0.8565 (ptp) cc_final: 0.8117 (ptt)
REVERT: A  548 MET cc_start: 0.7909 (mtt) cc_final: 0.7272 (mtt)
REVERT: A  557 ASN cc_start: 0.8078 (t0) cc_final: 0.7386 (m-40)
REVERT: A  565 LEU cc_start: 0.9036 (tp) cc_final: 0.8794 (tp)
REVERT: A  573 ILE cc_start: 0.9181 (mt) cc_final: 0.8920 (mt)
REVERT: A  617 GLN cc_start: 0.8843 (mm-40) cc_final: 0.7993 (mm-40)
REVERT: A  629 ASN cc_start: 0.9002 (m110) cc_final: 0.8665 (m-40)
REVERT: A  652 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8511 (tttt)
REVERT: B   71 MET cc_start: 0.7856 (mmm) cc_final: 0.7188 (mmm)
REVERT: B   96 ARG cc_start: 0.8166 (ttt180) cc_final: 0.7834 (mmm-85)
REVERT: B  105 ASP cc_start: 0.7906 (t70) cc_final: 0.7703 (t0)
REVERT: B  160 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7750 (tpt170)
REVERT: B  198 MET cc_start: 0.9076 (ttm) cc_final: 0.8591 (ttm)
REVERT: B  253 PHE cc_start: 0.7469 (m-80) cc_final: 0.7153 (m-80)
REVERT: B  458 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7521 (tp30)
REVERT: B  477 ASP cc_start: 0.8113 (t0) cc_final: 0.7907 (t0)
REVERT: B  514 MET cc_start: 0.8613 (ptp) cc_final: 0.8009 (ptt)
REVERT: B  523 MET cc_start: 0.8561 (tpt) cc_final: 0.8255 (tpt)
REVERT: B  585 GLU cc_start: 0.8573 (tp30) cc_final: 0.8359 (mm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 316
  average time/residue: 0.2018
  time to fit residues: 90.0548
Evaluate side-chains
  243 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0010
   chunk 15 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    2.5990

-------------------------------------------------------------------------------
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 424 GLN
A 457 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.150944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117359 restraints weight = 16760.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119872 restraints weight = 10399.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.121880 restraints weight = 7540.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9092  Z= 0.185
  Angle     :  0.672  11.296  12324  Z= 0.338
  Chirality :  0.042   0.146   1427
  Planarity :  0.005   0.070   1522
  Dihedral  :  6.913  46.833   1382
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.80 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.25 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.23), residues: 1116
  helix: -1.22 (0.19), residues: 604
  sheet: -1.02 (0.81), residues: 34
  loop : -3.06 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 379 
 HIS   0.009   0.002   HIS B 630 
 PHE   0.024   0.002   PHE B 506 
 TYR   0.015   0.002   TYR A 342 
 ARG   0.007   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  365)
  hydrogen bonds       : angle       4.85953 ( 1059)
  SS BOND              : bond        0.00405 (    3)
  SS BOND              : angle       0.89340 (    6)
  covalent geometry    : bond        0.00426 ( 9089)
  covalent geometry    : angle       0.67231 (12318)

*********************** 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
  297 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 296
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.7925 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8551 (tttt) cc_final: 0.8239 (ttpt)
REVERT: A  192 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8535 (mmmm)
REVERT: A  240 PHE cc_start: 0.8715 (p90) cc_final: 0.8274 (p90)
REVERT: A  430 LEU cc_start: 0.9436 (mt) cc_final: 0.9227 (mt)
REVERT: A  458 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7486 (mm-30)
REVERT: A  470 PHE cc_start: 0.8794 (t80) cc_final: 0.8546 (t80)
REVERT: A  489 PHE cc_start: 0.8002 (t80) cc_final: 0.7741 (t80)
REVERT: A  548 MET cc_start: 0.8252 (mtt) cc_final: 0.7977 (mtt)
REVERT: A  557 ASN cc_start: 0.8221 (t0) cc_final: 0.7792 (m-40)
REVERT: A  565 LEU cc_start: 0.9090 (tp) cc_final: 0.8838 (tp)
REVERT: A  617 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8051 (mm-40)
REVERT: A  629 ASN cc_start: 0.9030 (m110) cc_final: 0.8780 (m-40)
REVERT: A  652 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8425 (tttt)
REVERT: B   71 MET cc_start: 0.7867 (mmm) cc_final: 0.6988 (mmm)
REVERT: B   81 PRO cc_start: 0.7976 (Cg_endo) cc_final: 0.7753 (Cg_exo)
REVERT: B  143 SER cc_start: 0.8362 (p) cc_final: 0.8117 (p)
REVERT: B  160 ARG cc_start: 0.8720 (ttm110) cc_final: 0.7774 (tpt-90)
REVERT: B  238 ILE cc_start: 0.9293 (mp) cc_final: 0.9074 (mp)
REVERT: B  277 PHE cc_start: 0.6687 (m-80) cc_final: 0.6163 (m-80)
REVERT: B  346 LYS cc_start: 0.7565 (tptp) cc_final: 0.7361 (mtpp)
REVERT: B  424 GLN cc_start: 0.6976 (tt0) cc_final: 0.6721 (mt0)
REVERT: B  458 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7398 (mm-30)
REVERT: B  460 ILE cc_start: 0.9088 (tp) cc_final: 0.8788 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 297
  average time/residue: 0.1813
  time to fit residues: 76.9011
Evaluate side-chains
  229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 58 optimal weight:   20.0000
   chunk 90 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 109 optimal weight:    9.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 424 GLN
** 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 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 = 0.3861 r_free = 0.3861 target = 0.151992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117871 restraints weight = 16645.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120483 restraints weight = 10380.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.122356 restraints weight = 7524.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9092  Z= 0.151
  Angle     :  0.631   8.906  12324  Z= 0.315
  Chirality :  0.041   0.139   1427
  Planarity :  0.004   0.070   1522
  Dihedral  :  6.371  39.269   1382
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.23), residues: 1116
  helix: -0.89 (0.20), residues: 610
  sheet: -1.03 (0.80), residues: 34
  loop : -2.93 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 155 
 PHE   0.029   0.002   PHE A 489 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03301 (  365)
  hydrogen bonds       : angle       4.72389 ( 1059)
  SS BOND              : bond        0.00271 (    3)
  SS BOND              : angle       0.87852 (    6)
  covalent geometry    : bond        0.00355 ( 9089)
  covalent geometry    : angle       0.63036 (12318)

*********************** 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
  288 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7958 (mmt) cc_final: 0.7443 (mmm)
REVERT: A   81 PRO cc_start: 0.8462 (Cg_endo) cc_final: 0.8010 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8581 (tttt) cc_final: 0.8335 (ttpt)
REVERT: A  105 ASP cc_start: 0.7671 (t70) cc_final: 0.7430 (t0)
REVERT: A  141 GLN cc_start: 0.8270 (mp-120) cc_final: 0.7802 (mp10)
REVERT: A  192 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8654 (mmmm)
REVERT: A  240 PHE cc_start: 0.8669 (p90) cc_final: 0.8251 (p90)
REVERT: A  458 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7522 (mm-30)
REVERT: A  470 PHE cc_start: 0.8870 (t80) cc_final: 0.8617 (t80)
REVERT: A  514 MET cc_start: 0.8049 (ptp) cc_final: 0.7738 (ptt)
REVERT: A  557 ASN cc_start: 0.8298 (t0) cc_final: 0.7784 (m-40)
REVERT: A  565 LEU cc_start: 0.9103 (tp) cc_final: 0.8857 (tp)
REVERT: A  617 GLN cc_start: 0.8562 (mm-40) cc_final: 0.7941 (mm-40)
REVERT: A  629 ASN cc_start: 0.8985 (m110) cc_final: 0.8477 (m-40)
REVERT: A  652 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8470 (tttt)
REVERT: B   71 MET cc_start: 0.7772 (mmm) cc_final: 0.7108 (mmm)
REVERT: B   96 ARG cc_start: 0.8090 (mmt90) cc_final: 0.7876 (mmm-85)
REVERT: B  143 SER cc_start: 0.8389 (p) cc_final: 0.8152 (p)
REVERT: B  160 ARG cc_start: 0.8727 (ttm110) cc_final: 0.7803 (tpt-90)
REVERT: B  277 PHE cc_start: 0.6312 (m-80) cc_final: 0.5984 (m-80)
REVERT: B  346 LYS cc_start: 0.7707 (tptp) cc_final: 0.7383 (mtpp)
REVERT: B  424 GLN cc_start: 0.6822 (tt0) cc_final: 0.6549 (mt0)
REVERT: B  430 LEU cc_start: 0.9412 (mt) cc_final: 0.9190 (mt)
REVERT: B  460 ILE cc_start: 0.9099 (tp) cc_final: 0.8681 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.1746
  time to fit residues: 72.2689
Evaluate side-chains
  242 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 53 optimal weight:    0.0770
   chunk 96 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 100 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    1.1942

-------------------------------------------------------------------------------
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 267 HIS
A 283 HIS
A 391 ASN
A 424 GLN
A 630 HIS
** B 437 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 = 0.3882 r_free = 0.3882 target = 0.154362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.120307 restraints weight = 16515.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122940 restraints weight = 10402.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.124904 restraints weight = 7544.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3734

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     :  0.605   6.709  12324  Z= 0.301
  Chirality :  0.040   0.137   1427
  Planarity :  0.004   0.070   1522
  Dihedral  :  5.892  37.188   1382
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.24), residues: 1116
  helix: -0.66 (0.20), residues: 610
  sheet: -0.90 (0.76), residues: 34
  loop : -2.86 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 267 
 PHE   0.033   0.002   PHE A 489 
 TYR   0.014   0.001   TYR A 494 
 ARG   0.007   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03035 (  365)
  hydrogen bonds       : angle       4.54310 ( 1059)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       1.41400 (    6)
  covalent geometry    : bond        0.00289 ( 9089)
  covalent geometry    : angle       0.60412 (12318)

*********************** 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
  304 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 PRO cc_start: 0.8411 (Cg_endo) cc_final: 0.7982 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8554 (tttt) cc_final: 0.8304 (ttpt)
REVERT: A  105 ASP cc_start: 0.7627 (t70) cc_final: 0.7362 (t0)
REVERT: A  120 ASN cc_start: 0.8266 (p0) cc_final: 0.7560 (m110)
REVERT: A  141 GLN cc_start: 0.8342 (mp-120) cc_final: 0.7872 (mp10)
REVERT: A  143 SER cc_start: 0.7833 (p) cc_final: 0.7625 (p)
REVERT: A  187 SER cc_start: 0.8081 (m) cc_final: 0.7667 (p)
REVERT: A  192 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8728 (mmmm)
REVERT: A  240 PHE cc_start: 0.8651 (p90) cc_final: 0.8212 (p90)
REVERT: A  384 SER cc_start: 0.9267 (t) cc_final: 0.8983 (t)
REVERT: A  458 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A  514 MET cc_start: 0.8009 (ptp) cc_final: 0.7723 (ptt)
REVERT: A  557 ASN cc_start: 0.8291 (t0) cc_final: 0.7905 (m-40)
REVERT: A  565 LEU cc_start: 0.9080 (tp) cc_final: 0.8858 (tp)
REVERT: A  617 GLN cc_start: 0.8565 (mm-40) cc_final: 0.7959 (mm-40)
REVERT: A  652 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8443 (tttt)
REVERT: B   71 MET cc_start: 0.7737 (mmm) cc_final: 0.6963 (mmm)
REVERT: B  105 ASP cc_start: 0.7439 (t0) cc_final: 0.7225 (p0)
REVERT: B  143 SER cc_start: 0.8346 (p) cc_final: 0.8098 (p)
REVERT: B  152 MET cc_start: 0.6668 (ptp) cc_final: 0.6323 (ptp)
REVERT: B  160 ARG cc_start: 0.8824 (ttm110) cc_final: 0.7982 (tpt-90)
REVERT: B  277 PHE cc_start: 0.6472 (m-80) cc_final: 0.6047 (m-80)
REVERT: B  342 TYR cc_start: 0.7349 (t80) cc_final: 0.6830 (t80)
REVERT: B  346 LYS cc_start: 0.7716 (tptp) cc_final: 0.7370 (mtpp)
REVERT: B  424 GLN cc_start: 0.6769 (tt0) cc_final: 0.6511 (mt0)
REVERT: B  430 LEU cc_start: 0.9405 (mt) cc_final: 0.9198 (mt)
REVERT: B  470 PHE cc_start: 0.8850 (t80) cc_final: 0.8493 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 304
  average time/residue: 0.1763
  time to fit residues: 76.6161
Evaluate side-chains
  239 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    0.0870
   chunk 24 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 1 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 108 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.9364

-------------------------------------------------------------------------------
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 630 HIS
B 222 ASN
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.152640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119183 restraints weight = 16655.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.121884 restraints weight = 10423.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123804 restraints weight = 7536.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9092  Z= 0.149
  Angle     :  0.639  10.701  12324  Z= 0.317
  Chirality :  0.042   0.181   1427
  Planarity :  0.004   0.070   1522
  Dihedral  :  5.924  40.536   1382
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.24), residues: 1116
  helix: -0.48 (0.21), residues: 600
  sheet: -0.90 (0.76), residues: 34
  loop : -2.84 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 630 
 PHE   0.031   0.002   PHE A 489 
 TYR   0.017   0.002   TYR B 464 
 ARG   0.008   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  365)
  hydrogen bonds       : angle       4.59487 ( 1059)
  SS BOND              : bond        0.00453 (    3)
  SS BOND              : angle       1.18022 (    6)
  covalent geometry    : bond        0.00352 ( 9089)
  covalent geometry    : angle       0.63880 (12318)

*********************** 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
  287 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 287
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 PRO cc_start: 0.8443 (Cg_endo) cc_final: 0.7892 (Cg_exo)
REVERT: A   86 LYS cc_start: 0.8604 (tttt) cc_final: 0.7935 (pttt)
REVERT: A  105 ASP cc_start: 0.7708 (t70) cc_final: 0.7418 (t0)
REVERT: A  120 ASN cc_start: 0.8268 (p0) cc_final: 0.7586 (m110)
REVERT: A  141 GLN cc_start: 0.8092 (mp-120) cc_final: 0.7793 (mp10)
REVERT: A  143 SER cc_start: 0.7948 (p) cc_final: 0.7723 (p)
REVERT: A  187 SER cc_start: 0.8093 (m) cc_final: 0.7665 (p)
REVERT: A  192 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8719 (mmmm)
REVERT: A  240 PHE cc_start: 0.8730 (p90) cc_final: 0.8324 (p90)
REVERT: A  346 LYS cc_start: 0.7681 (tptp) cc_final: 0.7318 (mtpp)
REVERT: A  430 LEU cc_start: 0.9319 (mt) cc_final: 0.9107 (mt)
REVERT: A  458 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  514 MET cc_start: 0.8124 (ptp) cc_final: 0.7740 (ptt)
REVERT: A  557 ASN cc_start: 0.8292 (t0) cc_final: 0.7763 (m-40)
REVERT: A  565 LEU cc_start: 0.9144 (tp) cc_final: 0.8912 (tp)
REVERT: A  617 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7958 (mm-40)
REVERT: A  629 ASN cc_start: 0.8934 (m110) cc_final: 0.8386 (m-40)
REVERT: A  652 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8434 (tttt)
REVERT: B   71 MET cc_start: 0.7654 (mmm) cc_final: 0.6888 (mmm)
REVERT: B   96 ARG cc_start: 0.8040 (mmt90) cc_final: 0.7839 (mmm-85)
REVERT: B  105 ASP cc_start: 0.7545 (t0) cc_final: 0.7312 (t0)
REVERT: B  152 MET cc_start: 0.6507 (ptp) cc_final: 0.6123 (ptp)
REVERT: B  160 ARG cc_start: 0.8862 (ttm110) cc_final: 0.7987 (tpt-90)
REVERT: B  199 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6813 (mm-30)
REVERT: B  238 ILE cc_start: 0.9219 (mp) cc_final: 0.9010 (mp)
REVERT: B  277 PHE cc_start: 0.6397 (m-80) cc_final: 0.6137 (m-80)
REVERT: B  342 TYR cc_start: 0.7480 (t80) cc_final: 0.7128 (t80)
REVERT: B  346 LYS cc_start: 0.7859 (tptp) cc_final: 0.7545 (mtpp)
REVERT: B  424 GLN cc_start: 0.6776 (tt0) cc_final: 0.6524 (mt0)
REVERT: B  430 LEU cc_start: 0.9374 (mt) cc_final: 0.9163 (mt)
REVERT: B  514 MET cc_start: 0.8136 (ptp) cc_final: 0.7707 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 287
  average time/residue: 0.1843
  time to fit residues: 74.6439
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  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    0.0040
   chunk 97 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    3.0000

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
A 267 HIS
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3816 r_free = 0.3816 target = 0.149029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114997 restraints weight = 17086.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117671 restraints weight = 10598.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119526 restraints weight = 7647.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9092  Z= 0.198
  Angle     :  0.688   9.905  12324  Z= 0.342
  Chirality :  0.044   0.257   1427
  Planarity :  0.004   0.061   1522
  Dihedral  :  6.377  46.389   1382
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.25), residues: 1116
  helix: -0.43 (0.21), residues: 600
  sheet: -0.87 (0.82), residues: 34
  loop : -2.83 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 267 
 PHE   0.030   0.002   PHE A 489 
 TYR   0.020   0.002   TYR A 464 
 ARG   0.012   0.001   ARG A 482 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03403 (  365)
  hydrogen bonds       : angle       4.67672 ( 1059)
  SS BOND              : bond        0.00673 (    3)
  SS BOND              : angle       1.12082 (    6)
  covalent geometry    : bond        0.00459 ( 9089)
  covalent geometry    : angle       0.68768 (12318)

*********************** 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
  279 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LYS cc_start: 0.7967 (tttp) cc_final: 0.7761 (ttmm)
REVERT: A   81 PRO cc_start: 0.8447 (Cg_endo) cc_final: 0.8064 (Cg_exo)
REVERT: A  120 ASN cc_start: 0.8120 (p0) cc_final: 0.7459 (m-40)
REVERT: A  141 GLN cc_start: 0.8356 (mp-120) cc_final: 0.7863 (mp10)
REVERT: A  187 SER cc_start: 0.8139 (m) cc_final: 0.7715 (p)
REVERT: A  192 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8850 (mmmm)
REVERT: A  240 PHE cc_start: 0.8898 (p90) cc_final: 0.8506 (p90)
REVERT: A  265 MET cc_start: 0.7734 (mmp) cc_final: 0.7293 (mmm)
REVERT: A  276 TYR cc_start: 0.7473 (t80) cc_final: 0.6689 (t80)
REVERT: A  346 LYS cc_start: 0.7734 (tptp) cc_final: 0.7358 (mtpp)
REVERT: A  458 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7596 (mm-30)
REVERT: A  470 PHE cc_start: 0.8849 (t80) cc_final: 0.8561 (t80)
REVERT: A  514 MET cc_start: 0.8207 (ptp) cc_final: 0.7794 (ptt)
REVERT: B   71 MET cc_start: 0.7681 (mmm) cc_final: 0.6858 (mmm)
REVERT: B  105 ASP cc_start: 0.7580 (t0) cc_final: 0.7327 (t0)
REVERT: B  152 MET cc_start: 0.6343 (ptp) cc_final: 0.6047 (ptp)
REVERT: B  160 ARG cc_start: 0.8880 (ttm110) cc_final: 0.8005 (tpt-90)
REVERT: B  199 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6834 (mm-30)
REVERT: B  238 ILE cc_start: 0.9247 (mp) cc_final: 0.9036 (mp)
REVERT: B  276 TYR cc_start: 0.7890 (t80) cc_final: 0.7225 (t80)
REVERT: B  346 LYS cc_start: 0.7908 (tptp) cc_final: 0.7620 (mtpp)
REVERT: B  514 MET cc_start: 0.8179 (ptp) cc_final: 0.7683 (ptt)
REVERT: B  629 ASN cc_start: 0.9012 (m110) cc_final: 0.8393 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1876
  time to fit residues: 73.8819
Evaluate side-chains
  232 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 232
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 57 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 HIS
A 398 GLN
A 424 GLN
** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.151743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117784 restraints weight = 17129.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.120507 restraints weight = 10604.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.122402 restraints weight = 7626.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.4325

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= 0.144
  Angle     :  0.671  10.095  12324  Z= 0.329
  Chirality :  0.042   0.241   1427
  Planarity :  0.004   0.065   1522
  Dihedral  :  6.101  45.526   1382
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.25), residues: 1116
  helix: -0.30 (0.21), residues: 588
  sheet: -0.72 (0.82), residues: 34
  loop : -2.80 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 630 
 PHE   0.026   0.002   PHE B 489 
 TYR   0.018   0.002   TYR A 464 
 ARG   0.008   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  365)
  hydrogen bonds       : angle       4.62927 ( 1059)
  SS BOND              : bond        0.00323 (    3)
  SS BOND              : angle       1.03273 (    6)
  covalent geometry    : bond        0.00343 ( 9089)
  covalent geometry    : angle       0.67056 (12318)

*********************** 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
  274 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 CYS cc_start: 0.7296 (t) cc_final: 0.6937 (t)
REVERT: A  120 ASN cc_start: 0.7884 (p0) cc_final: 0.7373 (m-40)
REVERT: A  141 GLN cc_start: 0.8065 (mp-120) cc_final: 0.7718 (mp10)
REVERT: A  187 SER cc_start: 0.8213 (m) cc_final: 0.7778 (p)
REVERT: A  192 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8772 (mmmm)
REVERT: A  199 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7225 (mm-30)
REVERT: A  240 PHE cc_start: 0.8799 (p90) cc_final: 0.8348 (p90)
REVERT: A  265 MET cc_start: 0.7653 (mmp) cc_final: 0.7308 (mmm)
REVERT: A  276 TYR cc_start: 0.7403 (t80) cc_final: 0.6597 (t80)
REVERT: A  277 PHE cc_start: 0.6385 (m-80) cc_final: 0.5936 (m-80)
REVERT: A  346 LYS cc_start: 0.7691 (tptp) cc_final: 0.7329 (mtpp)
REVERT: A  458 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7575 (mm-30)
REVERT: A  514 MET cc_start: 0.8123 (ptp) cc_final: 0.7791 (ptt)
REVERT: A  557 ASN cc_start: 0.8780 (t0) cc_final: 0.8499 (t0)
REVERT: B   71 MET cc_start: 0.7645 (mmm) cc_final: 0.6790 (mmm)
REVERT: B  105 ASP cc_start: 0.7567 (t0) cc_final: 0.7095 (p0)
REVERT: B  152 MET cc_start: 0.6230 (ptp) cc_final: 0.5989 (ptp)
REVERT: B  160 ARG cc_start: 0.8835 (ttm110) cc_final: 0.8025 (tpt-90)
REVERT: B  199 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6728 (mm-30)
REVERT: B  233 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8290 (mtmt)
REVERT: B  238 ILE cc_start: 0.9221 (mp) cc_final: 0.9008 (mp)
REVERT: B  276 TYR cc_start: 0.7812 (t80) cc_final: 0.7070 (t80)
REVERT: B  346 LYS cc_start: 0.7888 (tptp) cc_final: 0.7647 (mtpp)
REVERT: B  490 THR cc_start: 0.8552 (p) cc_final: 0.8275 (p)
REVERT: B  581 LEU cc_start: 0.9531 (mp) cc_final: 0.9296 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 274
  average time/residue: 0.1779
  time to fit residues: 69.7727
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  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 30 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 HIS
A 283 HIS
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 557 ASN
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.155281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.122234 restraints weight = 16802.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.125000 restraints weight = 10390.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126947 restraints weight = 7477.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9092  Z= 0.116
  Angle     :  0.663   9.408  12324  Z= 0.321
  Chirality :  0.042   0.200   1427
  Planarity :  0.004   0.061   1522
  Dihedral  :  5.673  42.342   1382
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.25), residues: 1116
  helix: -0.38 (0.21), residues: 622
  sheet: -0.69 (0.81), residues: 34
  loop : -2.61 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.003   0.000   HIS A 267 
 PHE   0.030   0.002   PHE B 545 
 TYR   0.014   0.001   TYR B 464 
 ARG   0.009   0.000   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03200 (  365)
  hydrogen bonds       : angle       4.54821 ( 1059)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       1.09926 (    6)
  covalent geometry    : bond        0.00276 ( 9089)
  covalent geometry    : angle       0.66276 (12318)

*********************** 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
  286 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 286
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 MET cc_start: 0.7797 (mmt) cc_final: 0.7586 (mmm)
REVERT: A  119 CYS cc_start: 0.7191 (t) cc_final: 0.6851 (t)
REVERT: A  120 ASN cc_start: 0.7737 (p0) cc_final: 0.7191 (m-40)
REVERT: A  134 LEU cc_start: 0.7625 (mp) cc_final: 0.7366 (tp)
REVERT: A  187 SER cc_start: 0.8188 (m) cc_final: 0.7728 (p)
REVERT: A  192 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8746 (mmmm)
REVERT: A  238 ILE cc_start: 0.9068 (mp) cc_final: 0.8706 (mp)
REVERT: A  240 PHE cc_start: 0.8676 (p90) cc_final: 0.8222 (p90)
REVERT: A  265 MET cc_start: 0.7523 (mmp) cc_final: 0.7201 (mmm)
REVERT: A  276 TYR cc_start: 0.7396 (t80) cc_final: 0.6602 (t80)
REVERT: A  277 PHE cc_start: 0.6308 (m-80) cc_final: 0.5959 (m-80)
REVERT: A  346 LYS cc_start: 0.7761 (tptp) cc_final: 0.7446 (mtpp)
REVERT: A  384 SER cc_start: 0.9190 (t) cc_final: 0.8987 (t)
REVERT: A  458 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7598 (mm-30)
REVERT: A  514 MET cc_start: 0.8115 (ptp) cc_final: 0.7714 (ptt)
REVERT: A  549 MET cc_start: 0.8259 (ttt) cc_final: 0.7949 (tmm)
REVERT: A  649 LEU cc_start: 0.8205 (tt) cc_final: 0.7973 (tt)
REVERT: B   71 MET cc_start: 0.7468 (mmm) cc_final: 0.6874 (mmm)
REVERT: B  105 ASP cc_start: 0.7452 (t0) cc_final: 0.7156 (p0)
REVERT: B  160 ARG cc_start: 0.8833 (ttm110) cc_final: 0.8054 (tpt-90)
REVERT: B  187 SER cc_start: 0.7989 (m) cc_final: 0.7618 (p)
REVERT: B  199 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6904 (mm-30)
REVERT: B  233 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8232 (mtmt)
REVERT: B  238 ILE cc_start: 0.9123 (mp) cc_final: 0.8902 (mp)
REVERT: B  277 PHE cc_start: 0.6551 (m-80) cc_final: 0.6343 (m-80)
REVERT: B  346 LYS cc_start: 0.7857 (tptp) cc_final: 0.7628 (mtpp)
REVERT: B  514 MET cc_start: 0.7896 (ptp) cc_final: 0.7504 (ptt)
REVERT: B  581 LEU cc_start: 0.9471 (mp) cc_final: 0.9201 (mt)
REVERT: B  629 ASN cc_start: 0.8913 (m110) cc_final: 0.8307 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 286
  average time/residue: 0.1864
  time to fit residues: 76.2105
Evaluate side-chains
  248 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    0.0970
   chunk 62 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9990
   chunk 68 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 283 HIS
A 424 GLN
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 630 HIS ** 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 = 0.3829 r_free = 0.3829 target = 0.149902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.118988 restraints weight = 16900.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119359 restraints weight = 11749.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.119929 restraints weight = 8150.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9092  Z= 0.190
  Angle     :  0.711  10.355  12324  Z= 0.352
  Chirality :  0.044   0.209   1427
  Planarity :  0.005   0.065   1522
  Dihedral  :  6.183  46.434   1382
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.25), residues: 1116
  helix: -0.36 (0.21), residues: 614
  sheet: -0.65 (0.84), residues: 34
  loop : -2.82 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 567 
 HIS   0.003   0.001   HIS A 243 
 PHE   0.026   0.002   PHE A 489 
 TYR   0.021   0.002   TYR A 464 
 ARG   0.010   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  365)
  hydrogen bonds       : angle       4.81924 ( 1059)
  SS BOND              : bond        0.00367 (    3)
  SS BOND              : angle       1.01948 (    6)
  covalent geometry    : bond        0.00445 ( 9089)
  covalent geometry    : angle       0.71108 (12318)

********************** 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
  267 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.7924 (p0) cc_final: 0.7610 (p0)
REVERT: A  187 SER cc_start: 0.8323 (m) cc_final: 0.7931 (p)
REVERT: A  192 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8755 (mmmm)
REVERT: A  199 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7128 (mm-30)
REVERT: A  240 PHE cc_start: 0.8824 (p90) cc_final: 0.8417 (p90)
REVERT: A  265 MET cc_start: 0.7705 (mmp) cc_final: 0.7201 (mmm)
REVERT: A  276 TYR cc_start: 0.7384 (t80) cc_final: 0.6683 (t80)
REVERT: A  277 PHE cc_start: 0.6337 (m-80) cc_final: 0.6042 (m-80)
REVERT: A  346 LYS cc_start: 0.7889 (tptp) cc_final: 0.7559 (mtpp)
REVERT: A  430 LEU cc_start: 0.9270 (mt) cc_final: 0.9000 (mt)
REVERT: A  458 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7516 (mm-30)
REVERT: A  514 MET cc_start: 0.8243 (ptp) cc_final: 0.7714 (ptt)
REVERT: A  604 ASN cc_start: 0.8035 (p0) cc_final: 0.7818 (p0)
REVERT: B   71 MET cc_start: 0.7609 (mmm) cc_final: 0.6873 (mmm)
REVERT: B   96 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7762 (mmm-85)
REVERT: B  105 ASP cc_start: 0.7755 (t0) cc_final: 0.7248 (p0)
REVERT: B  153 THR cc_start: 0.8995 (p) cc_final: 0.8443 (p)
REVERT: B  160 ARG cc_start: 0.8911 (ttm110) cc_final: 0.8101 (tpt-90)
REVERT: B  199 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6909 (mm-30)
REVERT: B  233 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8367 (mtmt)
REVERT: B  276 TYR cc_start: 0.7817 (t80) cc_final: 0.7122 (t80)
REVERT: B  346 LYS cc_start: 0.7943 (tptp) cc_final: 0.7671 (mtpp)
REVERT: B  430 LEU cc_start: 0.9464 (mt) cc_final: 0.9261 (mt)
REVERT: B  604 ASN cc_start: 0.8037 (p0) cc_final: 0.7668 (p0)
REVERT: B  605 TYR cc_start: 0.6528 (m-80) cc_final: 0.6268 (m-10)
REVERT: B  629 ASN cc_start: 0.9062 (m110) cc_final: 0.8513 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 267
  average time/residue: 0.1889
  time to fit residues: 72.3281
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  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 84 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 267 HIS
** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 424 GLN
** 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**
** B 630 HIS ** 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 = 0.3797 r_free = 0.3797 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115460 restraints weight = 17172.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.117556 restraints weight = 10951.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.118075 restraints weight = 7197.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.4638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9092  Z= 0.216
  Angle     :  0.749  10.824  12324  Z= 0.367
  Chirality :  0.045   0.190   1427
  Planarity :  0.005   0.069   1522
  Dihedral  :  6.481  48.291   1382
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.05 %
    Favored  : 90.95 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.62 %
    Favored  : 99.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.25), residues: 1116
  helix: -0.40 (0.21), residues: 614
  sheet: -0.82 (0.87), residues: 34
  loop : -2.80 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 379 
 HIS   0.008   0.001   HIS A 267 
 PHE   0.028   0.003   PHE A 506 
 TYR   0.018   0.002   TYR B 464 
 ARG   0.010   0.001   ARG B 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  365)
  hydrogen bonds       : angle       4.85595 ( 1059)
  SS BOND              : bond        0.00396 (    3)
  SS BOND              : angle       0.96002 (    6)
  covalent geometry    : bond        0.00502 ( 9089)
  covalent geometry    : angle       0.74876 (12318)

===============================================================================
Job complete
usr+sys time: 2986.26 seconds
wall clock time: 52 minutes 47.19 seconds (3167.19 seconds total)