Starting phenix.real_space_refine
on Thu Mar  5 16:17:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dxd_30905/03_2026/7dxd_30905.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.013 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Ca      4      9.91       5
     Zn      4      6.06       5
     S     132      5.16       5
     C   15424      2.51       5
     N    3792      2.21       5
     O    4272      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23628
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 732, 5870
          Classifications: {'peptide': 732}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 27, 'TRANS': 704}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 37
          Unusual residues: {' CA': 1, ' ZN': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1328  SG  CYS A 182      86.403  24.516  78.918  1.00143.63           S
  ATOM   1343  SG  CYS A 184      88.739  23.851  76.056  1.00140.89           S
  ATOM   1361  SG  CYS A 187      87.488  27.317  76.638  1.00138.90           S

  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 6.04, per 1000 atoms: 0.26
  Number of scatterers: 23628
  At special positions: 0
  Unit cell: (124.355, 124.355, 167.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     Ca      4     19.99
     S     132     16.00
     O    4272      8.00
     N    3792      7.00
     C   15424      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 902 "
        pdb="ZN    ZN A 902 " - pdb=" ND1 HIS A 178 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 182 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 184 "
        pdb="ZN    ZN A 902 " - pdb=" SG  CYS A 187 "
      pdb="  ZN B 902 "
        pdb="ZN    ZN B 902 " - pdb=" ND1 HIS B 178 "
        pdb="ZN    ZN B 902 " - pdb=" SG  CYS B 182 "
        pdb="ZN    ZN B 902 " - pdb=" SG  CYS B 184 "
        pdb="ZN    ZN B 902 " - pdb=" SG  CYS B 187 "
      pdb="  ZN C 902 "
        pdb="ZN    ZN C 902 " - pdb=" ND1 HIS C 178 "
        pdb="ZN    ZN C 902 " - pdb=" SG  CYS C 182 "
        pdb="ZN    ZN C 902 " - pdb=" SG  CYS C 184 "
        pdb="ZN    ZN C 902 " - pdb=" SG  CYS C 187 "
      pdb="  ZN D 902 "
        pdb="ZN    ZN D 902 " - pdb=" ND1 HIS D 178 "
        pdb="ZN    ZN D 902 " - pdb=" SG  CYS D 182 "
        pdb="ZN    ZN D 902 " - pdb=" SG  CYS D 184 "
        pdb="ZN    ZN D 902 " - pdb=" SG  CYS D 187 "
      Number of angles added : 12


  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5608

  Finding SS restraints...
    Secondary structure from input PDB file:
      152 helices and 0 sheets defined
      77.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 39 through 50
    Processing helix  chain 'A' and resid 64 through 72
    Processing helix  chain 'A' and resid 74 through 83
    Processing helix  chain 'A' and resid 89 through 101
    Processing helix  chain 'A' and resid 102 through 111
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 124 through 131
      removed outlier: 3.928A  pdb=" N   GLN A 131 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 159
    Processing helix  chain 'A' and resid 160 through 170
    Processing helix  chain 'A' and resid 184 through 194
    Processing helix  chain 'A' and resid 196 through 210
    Processing helix  chain 'A' and resid 211 through 219
      removed outlier: 3.971A  pdb=" N   SER A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 240
    Processing helix  chain 'A' and resid 243 through 264
      removed outlier: 3.614A  pdb=" N   LEU A 264 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 276
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 305 through 310
    Processing helix  chain 'A' and resid 311 through 323
    Processing helix  chain 'A' and resid 327 through 332
      removed outlier: 3.601A  pdb=" N   ARG A 330 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 358
      Proline residue:  A 349  - end of helix
    Processing helix  chain 'A' and resid 361 through 368
    Processing helix  chain 'A' and resid 369 through 392
      removed outlier: 3.805A  pdb=" N   ALA A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 423 through 448
    Processing helix  chain 'A' and resid 448 through 455
      removed outlier: 3.644A  pdb=" N   LEU A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLN A 455 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 493
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 510 through 512
      No H-bonds generated for 'chain 'A' and resid 510 through 512'
    Processing helix  chain 'A' and resid 521 through 538
    Processing helix  chain 'A' and resid 539 through 548
      removed outlier: 4.149A  pdb=" N   LEU A 545 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
      Proline residue:  A 546  - end of helix
    Processing helix  chain 'A' and resid 551 through 588
      removed outlier: 4.683A  pdb=" N   LYS A 567 " --> pdb=" O   LYS A 563 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   PHE A 568 " --> pdb=" O   ASP A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 612
    Processing helix  chain 'A' and resid 618 through 622
      removed outlier: 3.770A  pdb=" N   SER A 621 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A 622 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 618 through 622'
    Processing helix  chain 'A' and resid 628 through 663
    Processing helix  chain 'A' and resid 669 through 683
    Processing helix  chain 'A' and resid 761 through 784
    Processing helix  chain 'A' and resid 788 through 824
      removed outlier: 3.713A  pdb=" N   ILE A 795 " --> pdb=" O   GLU A 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 37
    Processing helix  chain 'B' and resid 39 through 50
    Processing helix  chain 'B' and resid 64 through 72
    Processing helix  chain 'B' and resid 74 through 83
    Processing helix  chain 'B' and resid 89 through 101
    Processing helix  chain 'B' and resid 102 through 111
    Processing helix  chain 'B' and resid 112 through 117
    Processing helix  chain 'B' and resid 124 through 131
      removed outlier: 3.928A  pdb=" N   GLN B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 159
    Processing helix  chain 'B' and resid 160 through 170
    Processing helix  chain 'B' and resid 184 through 194
    Processing helix  chain 'B' and resid 196 through 210
    Processing helix  chain 'B' and resid 211 through 219
      removed outlier: 3.970A  pdb=" N   SER B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 240
    Processing helix  chain 'B' and resid 243 through 264
      removed outlier: 3.613A  pdb=" N   LEU B 264 " --> pdb=" O   GLY B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 276
    Processing helix  chain 'B' and resid 294 through 303
    Processing helix  chain 'B' and resid 305 through 310
    Processing helix  chain 'B' and resid 311 through 323
    Processing helix  chain 'B' and resid 327 through 332
      removed outlier: 3.601A  pdb=" N   ARG B 330 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 358
      Proline residue:  B 349  - end of helix
    Processing helix  chain 'B' and resid 361 through 368
    Processing helix  chain 'B' and resid 369 through 392
      removed outlier: 3.805A  pdb=" N   ALA B 392 " --> pdb=" O   LEU B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
    Processing helix  chain 'B' and resid 423 through 448
    Processing helix  chain 'B' and resid 448 through 455
      removed outlier: 3.644A  pdb=" N   LEU B 454 " --> pdb=" O   ARG B 450 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLN B 455 " --> pdb=" O   GLU B 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 493
    Processing helix  chain 'B' and resid 504 through 509
    Processing helix  chain 'B' and resid 510 through 512
      No H-bonds generated for 'chain 'B' and resid 510 through 512'
    Processing helix  chain 'B' and resid 521 through 538
    Processing helix  chain 'B' and resid 539 through 548
      removed outlier: 4.150A  pdb=" N   LEU B 545 " --> pdb=" O   ALA B 542 " (cutoff:3.500A)
      Proline residue:  B 546  - end of helix
    Processing helix  chain 'B' and resid 551 through 588
      removed outlier: 4.683A  pdb=" N   LYS B 567 " --> pdb=" O   LYS B 563 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   PHE B 568 " --> pdb=" O   ASP B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 612
    Processing helix  chain 'B' and resid 618 through 622
      removed outlier: 3.769A  pdb=" N   SER B 621 " --> pdb=" O   GLU B 618 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL B 622 " --> pdb=" O   VAL B 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 618 through 622'
    Processing helix  chain 'B' and resid 628 through 663
    Processing helix  chain 'B' and resid 669 through 683
    Processing helix  chain 'B' and resid 761 through 784
    Processing helix  chain 'B' and resid 788 through 824
      removed outlier: 3.712A  pdb=" N   ILE B 795 " --> pdb=" O   GLU B 791 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 37
    Processing helix  chain 'C' and resid 39 through 50
    Processing helix  chain 'C' and resid 64 through 72
    Processing helix  chain 'C' and resid 74 through 83
    Processing helix  chain 'C' and resid 89 through 101
    Processing helix  chain 'C' and resid 102 through 111
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 124 through 131
      removed outlier: 3.929A  pdb=" N   GLN C 131 " --> pdb=" O   GLU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 159
    Processing helix  chain 'C' and resid 160 through 170
    Processing helix  chain 'C' and resid 184 through 194
    Processing helix  chain 'C' and resid 196 through 210
    Processing helix  chain 'C' and resid 211 through 219
      removed outlier: 3.970A  pdb=" N   SER C 219 " --> pdb=" O   LEU C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 240
    Processing helix  chain 'C' and resid 243 through 264
      removed outlier: 3.613A  pdb=" N   LEU C 264 " --> pdb=" O   GLY C 260 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 276
    Processing helix  chain 'C' and resid 294 through 303
    Processing helix  chain 'C' and resid 305 through 310
    Processing helix  chain 'C' and resid 311 through 323
    Processing helix  chain 'C' and resid 327 through 332
      removed outlier: 3.601A  pdb=" N   ARG C 330 " --> pdb=" O   SER C 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 333 through 358
      Proline residue:  C 349  - end of helix
    Processing helix  chain 'C' and resid 361 through 368
    Processing helix  chain 'C' and resid 369 through 392
      removed outlier: 3.805A  pdb=" N   ALA C 392 " --> pdb=" O   LEU C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 414 through 421
    Processing helix  chain 'C' and resid 423 through 448
    Processing helix  chain 'C' and resid 448 through 455
      removed outlier: 3.644A  pdb=" N   LEU C 454 " --> pdb=" O   ARG C 450 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLN C 455 " --> pdb=" O   GLU C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 455 through 493
    Processing helix  chain 'C' and resid 504 through 509
    Processing helix  chain 'C' and resid 510 through 512
      No H-bonds generated for 'chain 'C' and resid 510 through 512'
    Processing helix  chain 'C' and resid 521 through 538
    Processing helix  chain 'C' and resid 539 through 548
      removed outlier: 4.150A  pdb=" N   LEU C 545 " --> pdb=" O   ALA C 542 " (cutoff:3.500A)
      Proline residue:  C 546  - end of helix
    Processing helix  chain 'C' and resid 551 through 588
      removed outlier: 4.682A  pdb=" N   LYS C 567 " --> pdb=" O   LYS C 563 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   PHE C 568 " --> pdb=" O   ASP C 564 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 612
    Processing helix  chain 'C' and resid 618 through 622
      removed outlier: 3.768A  pdb=" N   SER C 621 " --> pdb=" O   GLU C 618 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL C 622 " --> pdb=" O   VAL C 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 618 through 622'
    Processing helix  chain 'C' and resid 628 through 663
    Processing helix  chain 'C' and resid 669 through 683
    Processing helix  chain 'C' and resid 761 through 784
    Processing helix  chain 'C' and resid 788 through 824
      removed outlier: 3.712A  pdb=" N   ILE C 795 " --> pdb=" O   GLU C 791 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 37
    Processing helix  chain 'D' and resid 39 through 50
    Processing helix  chain 'D' and resid 64 through 72
    Processing helix  chain 'D' and resid 74 through 83
    Processing helix  chain 'D' and resid 89 through 101
    Processing helix  chain 'D' and resid 102 through 111
    Processing helix  chain 'D' and resid 112 through 117
    Processing helix  chain 'D' and resid 124 through 131
      removed outlier: 3.929A  pdb=" N   GLN D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 159
    Processing helix  chain 'D' and resid 160 through 170
    Processing helix  chain 'D' and resid 184 through 194
    Processing helix  chain 'D' and resid 196 through 210
    Processing helix  chain 'D' and resid 211 through 219
      removed outlier: 3.971A  pdb=" N   SER D 219 " --> pdb=" O   LEU D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 240
    Processing helix  chain 'D' and resid 243 through 264
      removed outlier: 3.613A  pdb=" N   LEU D 264 " --> pdb=" O   GLY D 260 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 267 through 276
    Processing helix  chain 'D' and resid 294 through 303
    Processing helix  chain 'D' and resid 305 through 310
    Processing helix  chain 'D' and resid 311 through 323
    Processing helix  chain 'D' and resid 327 through 332
      removed outlier: 3.600A  pdb=" N   ARG D 330 " --> pdb=" O   SER D 327 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 333 through 358
      Proline residue:  D 349  - end of helix
    Processing helix  chain 'D' and resid 361 through 368
    Processing helix  chain 'D' and resid 369 through 392
      removed outlier: 3.805A  pdb=" N   ALA D 392 " --> pdb=" O   LEU D 388 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 423 through 448
    Processing helix  chain 'D' and resid 448 through 455
      removed outlier: 3.643A  pdb=" N   LEU D 454 " --> pdb=" O   ARG D 450 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLN D 455 " --> pdb=" O   GLU D 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 455 through 493
    Processing helix  chain 'D' and resid 504 through 509
    Processing helix  chain 'D' and resid 510 through 512
      No H-bonds generated for 'chain 'D' and resid 510 through 512'
    Processing helix  chain 'D' and resid 521 through 538
    Processing helix  chain 'D' and resid 539 through 548
      removed outlier: 4.150A  pdb=" N   LEU D 545 " --> pdb=" O   ALA D 542 " (cutoff:3.500A)
      Proline residue:  D 546  - end of helix
    Processing helix  chain 'D' and resid 551 through 588
      removed outlier: 4.683A  pdb=" N   LYS D 567 " --> pdb=" O   LYS D 563 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   PHE D 568 " --> pdb=" O   ASP D 564 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 612
    Processing helix  chain 'D' and resid 618 through 622
      removed outlier: 3.769A  pdb=" N   SER D 621 " --> pdb=" O   GLU D 618 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL D 622 " --> pdb=" O   VAL D 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 618 through 622'
    Processing helix  chain 'D' and resid 628 through 663
    Processing helix  chain 'D' and resid 669 through 683
    Processing helix  chain 'D' and resid 761 through 784
    Processing helix  chain 'D' and resid 788 through 824
      removed outlier: 3.712A  pdb=" N   ILE D 795 " --> pdb=" O   GLU D 791 " (cutoff:3.500A)

    1600 hydrogen bonds defined for protein.
    4740 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: 4.30

  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: 7376
        1.34 -     1.47: 5776
        1.47 -     1.59: 10776
        1.59 -     1.72: 4
        1.72 -     1.84: 216
  Bond restraints: 24148
  Sorted by residual:
  bond pdb=" CAY Y01 B 901 "
       pdb=" OAW Y01 B 901 "
    ideal  model  delta    sigma   weight residual
    1.332  1.466 -0.134 2.00e-02 2.50e+03 4.46e+01
  bond pdb=" CAY Y01 A 901 "
       pdb=" OAW Y01 A 901 "
    ideal  model  delta    sigma   weight residual
    1.332  1.465 -0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" CAY Y01 C 901 "
       pdb=" OAW Y01 C 901 "
    ideal  model  delta    sigma   weight residual
    1.332  1.465 -0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" CAY Y01 D 901 "
       pdb=" OAW Y01 D 901 "
    ideal  model  delta    sigma   weight residual
    1.332  1.465 -0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" CAX Y01 B 901 "
       pdb=" OAH Y01 B 901 "
    ideal  model  delta    sigma   weight residual
    1.248  1.330 -0.082 2.00e-02 2.50e+03 1.70e+01
  ... (remaining 24143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 32179
        2.03 -     4.06: 424
        4.06 -     6.09: 89
        6.09 -     8.12: 28
        8.12 -    10.15: 4
  Bond angle restraints: 32724
  Sorted by residual:
  angle pdb=" C   LEU B  24 "
        pdb=" CA  LEU B  24 "
        pdb=" CB  LEU B  24 "
      ideal   model   delta    sigma   weight residual
     116.54  110.56    5.98 1.15e+00 7.56e-01 2.70e+01
  angle pdb=" C   LEU A  24 "
        pdb=" CA  LEU A  24 "
        pdb=" CB  LEU A  24 "
      ideal   model   delta    sigma   weight residual
     116.54  110.56    5.98 1.15e+00 7.56e-01 2.70e+01
  angle pdb=" C   LEU C  24 "
        pdb=" CA  LEU C  24 "
        pdb=" CB  LEU C  24 "
      ideal   model   delta    sigma   weight residual
     116.54  110.56    5.98 1.15e+00 7.56e-01 2.70e+01
  angle pdb=" C   LEU D  24 "
        pdb=" CA  LEU D  24 "
        pdb=" CB  LEU D  24 "
      ideal   model   delta    sigma   weight residual
     116.54  110.58    5.96 1.15e+00 7.56e-01 2.68e+01
  angle pdb=" CA  LEU D  24 "
        pdb=" C   LEU D  24 "
        pdb=" N   THR D  25 "
      ideal   model   delta    sigma   weight residual
     119.52  115.45    4.07 7.90e-01 1.60e+00 2.65e+01
  ... (remaining 32719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 13244
       16.23 -    32.46: 1076
       32.46 -    48.69: 228
       48.69 -    64.92: 92
       64.92 -    81.15: 24
  Dihedral angle restraints: 14664
    sinusoidal: 6024
      harmonic: 8640
  Sorted by residual:
  dihedral pdb=" CA  ILE B 174 "
           pdb=" C   ILE B 174 "
           pdb=" N   GLU B 175 "
           pdb=" CA  GLU B 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.01  -24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  ILE A 174 "
           pdb=" C   ILE A 174 "
           pdb=" N   GLU A 175 "
           pdb=" CA  GLU A 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.02  -24.98     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  ILE C 174 "
           pdb=" C   ILE C 174 "
           pdb=" N   GLU C 175 "
           pdb=" CA  GLU C 175 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.05  -24.95     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 14661 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 3268
       0.058 -    0.116: 439
       0.116 -    0.173: 17
       0.173 -    0.231: 4
       0.231 -    0.289: 4
  Chirality restraints: 3732
  Sorted by residual:
  chirality pdb=" CB  ILE A 655 "
            pdb=" CA  ILE A 655 "
            pdb=" CG1 ILE A 655 "
            pdb=" CG2 ILE A 655 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CB  ILE B 655 "
            pdb=" CA  ILE B 655 "
            pdb=" CG1 ILE B 655 "
            pdb=" CG2 ILE B 655 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.09e+00
  chirality pdb=" CB  ILE C 655 "
            pdb=" CA  ILE C 655 "
            pdb=" CG1 ILE C 655 "
            pdb=" CG2 ILE C 655 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.07e+00
  ... (remaining 3729 not shown)

  Planarity restraints: 4076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 656 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   ALA B 656 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ALA B 656 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET B 657 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 656 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   ALA C 656 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ALA C 656 "    0.011 2.00e-02 2.50e+03
        pdb=" N   MET C 657 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 656 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.77e+00
        pdb=" C   ALA A 656 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ALA A 656 "    0.011 2.00e-02 2.50e+03
        pdb=" N   MET A 657 "    0.010 2.00e-02 2.50e+03
  ... (remaining 4073 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 5500
        2.79 -     3.32: 23849
        3.32 -     3.84: 39439
        3.84 -     4.37: 45856
        4.37 -     4.90: 77826
  Nonbonded interactions: 192470
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 214 "
            pdb=" OG  SER C 218 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   TYR B 214 "
            pdb=" OG  SER B 218 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   TYR D 214 "
            pdb=" OG  SER D 218 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   TYR A 214 "
            pdb=" OG  SER A 218 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NZ  LYS B 306 "
            pdb=" OE2 GLU B 672 "
     model   vdw
     2.299 3.120
  ... (remaining 192465 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:             0.020
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     25.340
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.166  24164  Z= 0.232
  Angle     :  0.678  14.678  32736  Z= 0.346
  Chirality :  0.039   0.289   3732
  Planarity :  0.004   0.035   4076
  Dihedral  : 13.513  81.154   9056
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  6.27 %
    Favored  : 92.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.14), residues: 2880
  helix:  0.09 (0.10), residues: 2044
  sheet:  None (None), residues: 0
  loop : -1.96 (0.20), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  44 
 TYR   0.012   0.001   TYR C 639 
 PHE   0.009   0.001   PHE C 381 
 TRP   0.010   0.001   TRP C 611 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (24148)
  covalent geometry    : angle       0.62860 (32724)
  hydrogen bonds       : bond        0.12762 ( 1600)
  hydrogen bonds       : angle       4.60219 ( 4740)
  metal coordination   : bond        0.13191 (   16)
  metal coordination   : angle      13.28790 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 369
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 MET cc_start: 0.9152 (ttp) cc_final: 0.8622 (tmm)
REVERT: B   15 PHE cc_start: 0.6702 (m-10) cc_final: 0.6493 (m-80)
REVERT: B  464 MET cc_start: 0.9151 (ttp) cc_final: 0.8625 (tmm)
REVERT: C  464 MET cc_start: 0.9151 (ttp) cc_final: 0.8627 (tmm)
REVERT: D   15 PHE cc_start: 0.6710 (m-10) cc_final: 0.6496 (m-80)
REVERT: D  464 MET cc_start: 0.9152 (ttp) cc_final: 0.8625 (tmm)
  outliers start: 32
  outliers final: 0
  residues processed: 393
  average time/residue: 0.1584
  time to fit residues: 100.5061
Evaluate side-chains
  178 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 197 optimal weight:    0.9980
   chunk 215 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 132 optimal weight:    3.9990
   chunk 261 optimal weight:    9.9990
   chunk 248 optimal weight:    6.9990
   chunk 207 optimal weight:    3.9990
   chunk 155 optimal weight:    3.9990
   chunk 244 optimal weight:    9.9990
   chunk 183 optimal weight:    6.9990
   chunk 111 optimal weight:   10.0000
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 413 GLN
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 652 ASN
A 659 ASN
** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 GLN
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
B 659 ASN
** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 413 GLN
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 652 ASN
C 659 ASN
** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 413 GLN
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 652 ASN
D 659 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.064774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.051346 restraints weight = 96905.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.053248 restraints weight = 52789.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.054569 restraints weight = 35392.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.055434 restraints weight = 27037.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056124 restraints weight = 22498.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  24164  Z= 0.174
  Angle     :  0.602   8.695  32736  Z= 0.313
  Chirality :  0.039   0.146   3732
  Planarity :  0.004   0.043   4076
  Dihedral  :  5.895  55.000   3432
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  :  8.93 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.15), residues: 2880
  helix:  1.47 (0.11), residues: 2112
  sheet:  None (None), residues: 0
  loop : -1.34 (0.23), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 330 
 TYR   0.016   0.001   TYR C 138 
 PHE   0.021   0.001   PHE A  15 
 TRP   0.014   0.002   TRP B 322 
 HIS   0.002   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (24148)
  covalent geometry    : angle       0.60138 (32724)
  hydrogen bonds       : bond        0.04905 ( 1600)
  hydrogen bonds       : angle       3.92670 ( 4740)
  metal coordination   : bond        0.00560 (   16)
  metal coordination   : angle       1.99381 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 171
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 MET cc_start: 0.8838 (mmm) cc_final: 0.8575 (mmm)
REVERT: A  252 MET cc_start: 0.8469 (tpp) cc_final: 0.8225 (tpp)
REVERT: A  464 MET cc_start: 0.9165 (ttp) cc_final: 0.8794 (tmm)
REVERT: A  572 PHE cc_start: 0.8421 (t80) cc_final: 0.6254 (t80)
REVERT: B  169 MET cc_start: 0.8840 (mmm) cc_final: 0.8582 (mmm)
REVERT: B  252 MET cc_start: 0.8462 (tpp) cc_final: 0.8219 (tpp)
REVERT: B  464 MET cc_start: 0.9168 (ttp) cc_final: 0.8791 (tmm)
REVERT: B  572 PHE cc_start: 0.8418 (t80) cc_final: 0.6247 (t80)
REVERT: C  169 MET cc_start: 0.8833 (mmm) cc_final: 0.8570 (mmm)
REVERT: C  464 MET cc_start: 0.9161 (ttp) cc_final: 0.8787 (tmm)
REVERT: C  572 PHE cc_start: 0.8421 (t80) cc_final: 0.6263 (t80)
REVERT: C  652 ASN cc_start: 0.8837 (t0) cc_final: 0.8588 (t0)
REVERT: D  169 MET cc_start: 0.8829 (mmm) cc_final: 0.8565 (mmm)
REVERT: D  252 MET cc_start: 0.8451 (tpp) cc_final: 0.8214 (tpp)
REVERT: D  464 MET cc_start: 0.9169 (ttp) cc_final: 0.8791 (tmm)
REVERT: D  572 PHE cc_start: 0.8422 (t80) cc_final: 0.6256 (t80)
REVERT: D  652 ASN cc_start: 0.8830 (t0) cc_final: 0.8576 (t0)
  outliers start: 64
  outliers final: 41
  residues processed: 227
  average time/residue: 0.1305
  time to fit residues: 50.9056
Evaluate side-chains
  175 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 134
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  573 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 LYS
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  573 ILE
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  502 THR
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  569 MET
Chi-restraints excluded: chain C residue  573 ILE
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  236 LEU
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  569 MET
Chi-restraints excluded: chain D residue  573 ILE
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 218 optimal weight:    3.9990
   chunk 226 optimal weight:    6.9990
   chunk 280 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 287 optimal weight:    4.9990
   chunk 223 optimal weight:    7.9990
   chunk 228 optimal weight:    0.9980
   chunk 155 optimal weight:    0.1980
   chunk 279 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.065269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.052006 restraints weight = 96510.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.053928 restraints weight = 52319.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.055276 restraints weight = 34803.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056162 restraints weight = 26449.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.056862 restraints weight = 21991.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  24164  Z= 0.119
  Angle     :  0.526   6.927  32736  Z= 0.271
  Chirality :  0.037   0.130   3732
  Planarity :  0.004   0.041   4076
  Dihedral  :  5.858  53.648   3432
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.11 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.15), residues: 2880
  helix:  2.03 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -1.21 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 330 
 TYR   0.011   0.001   TYR B  37 
 PHE   0.017   0.001   PHE C 572 
 TRP   0.010   0.001   TRP C 673 
 HIS   0.002   0.000   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (24148)
  covalent geometry    : angle       0.52568 (32724)
  hydrogen bonds       : bond        0.04467 ( 1600)
  hydrogen bonds       : angle       3.60628 ( 4740)
  metal coordination   : bond        0.00323 (   16)
  metal coordination   : angle       1.52988 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 138
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 MET cc_start: 0.8548 (tpp) cc_final: 0.8326 (tpp)
REVERT: A  464 MET cc_start: 0.9123 (ttp) cc_final: 0.8549 (tmm)
REVERT: B  252 MET cc_start: 0.8551 (tpp) cc_final: 0.8325 (tpp)
REVERT: B  464 MET cc_start: 0.9128 (ttp) cc_final: 0.8557 (tmm)
REVERT: B  782 LYS cc_start: 0.9408 (tppt) cc_final: 0.9137 (tppt)
REVERT: C  464 MET cc_start: 0.9125 (ttp) cc_final: 0.8554 (tmm)
REVERT: D  252 MET cc_start: 0.8542 (tpp) cc_final: 0.8327 (tpp)
REVERT: D  464 MET cc_start: 0.9129 (ttp) cc_final: 0.8558 (tmm)
REVERT: D  782 LYS cc_start: 0.9452 (tppt) cc_final: 0.9215 (tppt)
  outliers start: 70
  outliers final: 28
  residues processed: 199
  average time/residue: 0.1306
  time to fit residues: 44.4495
Evaluate side-chains
  162 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  223 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  203 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  236 LEU
Chi-restraints excluded: chain C residue  502 THR
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  236 LEU
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 218 optimal weight:    9.9990
   chunk 121 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 185 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 125 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0770
   chunk 94 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 276 optimal weight:    0.9990
   chunk 181 optimal weight:    5.9990
   overall best weight:    2.3744

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 ASN
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 ASN
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 276 ASN
** D 523 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 = 0.3262 r_free = 0.3262 target = 0.063582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.050357 restraints weight = 97389.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.052206 restraints weight = 53376.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.053441 restraints weight = 36058.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.054398 restraints weight = 27678.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.054976 restraints weight = 22864.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  24164  Z= 0.143
  Angle     :  0.524   7.159  32736  Z= 0.270
  Chirality :  0.037   0.131   3732
  Planarity :  0.004   0.041   4076
  Dihedral  :  5.802  53.655   3432
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.13 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.16), residues: 2880
  helix:  2.35 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -1.04 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 330 
 TYR   0.013   0.001   TYR C  37 
 PHE   0.012   0.001   PHE A 568 
 TRP   0.014   0.001   TRP D 432 
 HIS   0.002   0.000   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (24148)
  covalent geometry    : angle       0.52340 (32724)
  hydrogen bonds       : bond        0.04386 ( 1600)
  hydrogen bonds       : angle       3.54125 ( 4740)
  metal coordination   : bond        0.00292 (   16)
  metal coordination   : angle       1.56158 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 138
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 MET cc_start: 0.8340 (tmm) cc_final: 0.8123 (tmm)
REVERT: A  464 MET cc_start: 0.9118 (ttp) cc_final: 0.8587 (tmm)
REVERT: A  572 PHE cc_start: 0.8613 (t80) cc_final: 0.7931 (t80)
REVERT: B  430 MET cc_start: 0.8355 (tmm) cc_final: 0.8143 (tmm)
REVERT: B  464 MET cc_start: 0.9115 (ttp) cc_final: 0.8586 (tmm)
REVERT: B  572 PHE cc_start: 0.8610 (t80) cc_final: 0.7919 (t80)
REVERT: C  430 MET cc_start: 0.8336 (tmm) cc_final: 0.8121 (tmm)
REVERT: C  464 MET cc_start: 0.9117 (ttp) cc_final: 0.8592 (tmm)
REVERT: C  572 PHE cc_start: 0.8606 (t80) cc_final: 0.7938 (t80)
REVERT: D  430 MET cc_start: 0.8360 (tmm) cc_final: 0.8145 (tmm)
REVERT: D  464 MET cc_start: 0.9120 (ttp) cc_final: 0.8594 (tmm)
REVERT: D  572 PHE cc_start: 0.8608 (t80) cc_final: 0.7935 (t80)
REVERT: D  782 LYS cc_start: 0.9441 (tppt) cc_final: 0.9218 (tppt)
  outliers start: 52
  outliers final: 29
  residues processed: 186
  average time/residue: 0.1323
  time to fit residues: 42.7277
Evaluate side-chains
  154 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  502 THR
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  569 MET
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  569 MET
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 142 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 171 optimal weight:    2.9990
   chunk 291 optimal weight:    5.9990
   chunk 91 optimal weight:    8.9990
   chunk 284 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 183 optimal weight:    0.0010
   chunk 174 optimal weight:    0.9990
   overall best weight:    2.5994

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.062809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.049739 restraints weight = 97972.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.051541 restraints weight = 53918.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.052741 restraints weight = 36454.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.053666 restraints weight = 28103.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054187 restraints weight = 23318.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  24164  Z= 0.148
  Angle     :  0.515   7.988  32736  Z= 0.267
  Chirality :  0.037   0.133   3732
  Planarity :  0.004   0.040   4076
  Dihedral  :  5.770  54.324   3432
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.91 %
    Favored  : 85.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.16), residues: 2880
  helix:  2.47 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -0.91 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 296 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.015   0.001   PHE B 568 
 TRP   0.012   0.002   TRP D 322 
 HIS   0.003   0.001   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (24148)
  covalent geometry    : angle       0.51405 (32724)
  hydrogen bonds       : bond        0.04367 ( 1600)
  hydrogen bonds       : angle       3.52364 ( 4740)
  metal coordination   : bond        0.00374 (   16)
  metal coordination   : angle       1.40214 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 126
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  274 ILE cc_start: 0.9566 (mm) cc_final: 0.9278 (tt)
REVERT: A  427 MET cc_start: 0.8938 (mmt) cc_final: 0.8690 (mmt)
REVERT: A  430 MET cc_start: 0.8395 (tmm) cc_final: 0.8150 (tmm)
REVERT: A  464 MET cc_start: 0.9113 (ttp) cc_final: 0.8593 (tmm)
REVERT: A  572 PHE cc_start: 0.8510 (t80) cc_final: 0.8154 (t80)
REVERT: B  274 ILE cc_start: 0.9557 (mm) cc_final: 0.9276 (tt)
REVERT: B  430 MET cc_start: 0.8410 (tmm) cc_final: 0.8142 (tmm)
REVERT: B  464 MET cc_start: 0.9124 (ttp) cc_final: 0.8595 (tmm)
REVERT: B  572 PHE cc_start: 0.8503 (t80) cc_final: 0.8152 (t80)
REVERT: C  274 ILE cc_start: 0.9559 (mm) cc_final: 0.9283 (tt)
REVERT: C  427 MET cc_start: 0.8938 (mmt) cc_final: 0.8689 (mmt)
REVERT: C  430 MET cc_start: 0.8387 (tmm) cc_final: 0.8116 (tmm)
REVERT: C  464 MET cc_start: 0.9114 (ttp) cc_final: 0.8591 (tmm)
REVERT: C  572 PHE cc_start: 0.8528 (t80) cc_final: 0.8201 (t80)
REVERT: D  274 ILE cc_start: 0.9554 (mm) cc_final: 0.9282 (tt)
REVERT: D  427 MET cc_start: 0.8920 (mmt) cc_final: 0.8675 (mmt)
REVERT: D  430 MET cc_start: 0.8397 (tmm) cc_final: 0.8150 (tmm)
REVERT: D  464 MET cc_start: 0.9116 (ttp) cc_final: 0.8592 (tmm)
REVERT: D  572 PHE cc_start: 0.8527 (t80) cc_final: 0.8206 (t80)
REVERT: D  782 LYS cc_start: 0.9425 (tppt) cc_final: 0.9199 (tppt)
  outliers start: 54
  outliers final: 30
  residues processed: 171
  average time/residue: 0.1361
  time to fit residues: 40.0942
Evaluate side-chains
  153 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  502 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  203 ILE
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 244 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 267 optimal weight:    2.9990
   chunk 123 optimal weight:    0.9980
   chunk 271 optimal weight:    2.9990
   chunk 215 optimal weight:    5.9990
   chunk 283 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 243 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.063264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.050313 restraints weight = 99728.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.052106 restraints weight = 54689.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.053375 restraints weight = 37063.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.054169 restraints weight = 28361.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.054797 restraints weight = 23779.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  24164  Z= 0.120
  Angle     :  0.487   7.266  32736  Z= 0.254
  Chirality :  0.037   0.127   3732
  Planarity :  0.004   0.039   4076
  Dihedral  :  5.803  56.721   3432
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.15 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.70 (0.16), residues: 2880
  helix:  2.63 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -0.73 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  44 
 TYR   0.011   0.001   TYR C  37 
 PHE   0.026   0.001   PHE D 568 
 TRP   0.011   0.001   TRP C 322 
 HIS   0.002   0.001   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (24148)
  covalent geometry    : angle       0.48627 (32724)
  hydrogen bonds       : bond        0.04114 ( 1600)
  hydrogen bonds       : angle       3.40503 ( 4740)
  metal coordination   : bond        0.00189 (   16)
  metal coordination   : angle       1.08486 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.8911 (mmt) cc_final: 0.8654 (mmt)
REVERT: A  430 MET cc_start: 0.8432 (tmm) cc_final: 0.8170 (tmm)
REVERT: A  464 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8615 (tmm)
REVERT: B  430 MET cc_start: 0.8449 (tmm) cc_final: 0.8166 (tmm)
REVERT: B  464 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8599 (tmm)
REVERT: B  572 PHE cc_start: 0.8448 (t80) cc_final: 0.8246 (t80)
REVERT: C  427 MET cc_start: 0.8912 (mmt) cc_final: 0.8652 (mmt)
REVERT: C  430 MET cc_start: 0.8431 (tmm) cc_final: 0.8169 (tmm)
REVERT: C  464 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8612 (tmm)
REVERT: C  572 PHE cc_start: 0.8526 (t80) cc_final: 0.8300 (t80)
REVERT: D  427 MET cc_start: 0.8914 (mmt) cc_final: 0.8651 (mmt)
REVERT: D  430 MET cc_start: 0.8434 (tmm) cc_final: 0.8180 (tmm)
REVERT: D  464 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8612 (tmm)
REVERT: D  572 PHE cc_start: 0.8517 (t80) cc_final: 0.8310 (t80)
  outliers start: 37
  outliers final: 29
  residues processed: 166
  average time/residue: 0.1346
  time to fit residues: 38.8994
Evaluate side-chains
  160 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  464 MET
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  464 MET
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  659 ASN
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  464 MET
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 255 optimal weight:    0.1980
   chunk 51 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 114 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 190 optimal weight:    0.9980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 652 ASN
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.063765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.050761 restraints weight = 97796.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.052592 restraints weight = 53593.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.053876 restraints weight = 36240.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.054766 restraints weight = 27674.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.055305 restraints weight = 22946.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  24164  Z= 0.105
  Angle     :  0.485   7.476  32736  Z= 0.251
  Chirality :  0.036   0.126   3732
  Planarity :  0.004   0.039   4076
  Dihedral  :  5.839  58.769   3432
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.34 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.16), residues: 2880
  helix:  2.68 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -0.62 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  44 
 TYR   0.009   0.001   TYR B  37 
 PHE   0.033   0.001   PHE D 568 
 TRP   0.011   0.001   TRP A 322 
 HIS   0.001   0.000   HIS C 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (24148)
  covalent geometry    : angle       0.48445 (32724)
  hydrogen bonds       : bond        0.03976 ( 1600)
  hydrogen bonds       : angle       3.37357 ( 4740)
  metal coordination   : bond        0.00171 (   16)
  metal coordination   : angle       0.97549 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 143
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.8862 (mmt) cc_final: 0.8450 (mmm)
REVERT: A  430 MET cc_start: 0.8431 (tmm) cc_final: 0.8159 (tmm)
REVERT: A  464 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8599 (tmm)
REVERT: B  427 MET cc_start: 0.8839 (mmm) cc_final: 0.8401 (mmm)
REVERT: B  430 MET cc_start: 0.8414 (tmm) cc_final: 0.8141 (tmm)
REVERT: B  464 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8592 (tmm)
REVERT: C  427 MET cc_start: 0.8855 (mmt) cc_final: 0.8442 (mmm)
REVERT: C  430 MET cc_start: 0.8426 (tmm) cc_final: 0.8155 (tmm)
REVERT: C  464 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8592 (tmm)
REVERT: D  427 MET cc_start: 0.8858 (mmt) cc_final: 0.8608 (mmm)
REVERT: D  430 MET cc_start: 0.8431 (tmm) cc_final: 0.8143 (tmm)
REVERT: D  464 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8595 (tmm)
REVERT: D  659 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.7855 (m110)
  outliers start: 50
  outliers final: 33
  residues processed: 182
  average time/residue: 0.1263
  time to fit residues: 40.2007
Evaluate side-chains
  171 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  657 MET
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  464 MET
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  464 MET
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  569 MET
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  464 MET
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  659 ASN
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 194 optimal weight:   10.0000
   chunk 160 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 83 optimal weight:    0.1980
   chunk 137 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 263 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0020
   chunk 57 optimal weight:    0.0980
   chunk 182 optimal weight:   10.0000
   chunk 278 optimal weight:    9.9990
   overall best weight:    0.8590

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

Flipped N/Q/H residues before XYZ refinement:
A  86 ASN
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 652 ASN
B  86 ASN
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.064383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.051387 restraints weight = 98586.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.053198 restraints weight = 54910.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.054472 restraints weight = 37283.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.055325 restraints weight = 28731.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.055849 restraints weight = 23949.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  24164  Z= 0.102
  Angle     :  0.476   7.404  32736  Z= 0.248
  Chirality :  0.036   0.167   3732
  Planarity :  0.004   0.040   4076
  Dihedral  :  5.891  59.807   3432
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.01 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.86 (0.16), residues: 2880
  helix:  2.71 (0.11), residues: 2120
  sheet:  None (None), residues: 0
  loop : -0.56 (0.23), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 330 
 TYR   0.009   0.001   TYR C  37 
 PHE   0.035   0.001   PHE C 568 
 TRP   0.011   0.001   TRP A 322 
 HIS   0.001   0.000   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (24148)
  covalent geometry    : angle       0.47590 (32724)
  hydrogen bonds       : bond        0.03843 ( 1600)
  hydrogen bonds       : angle       3.37977 ( 4740)
  metal coordination   : bond        0.00147 (   16)
  metal coordination   : angle       0.95421 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.8795 (mmt) cc_final: 0.8542 (mmm)
REVERT: A  430 MET cc_start: 0.8489 (tmm) cc_final: 0.8185 (tmm)
REVERT: A  464 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8592 (tmm)
REVERT: B  430 MET cc_start: 0.8391 (tmm) cc_final: 0.8118 (tmm)
REVERT: B  464 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8585 (tmm)
REVERT: C  427 MET cc_start: 0.8791 (mmt) cc_final: 0.8536 (mmm)
REVERT: C  430 MET cc_start: 0.8486 (tmm) cc_final: 0.8181 (tmm)
REVERT: C  464 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8589 (tmm)
REVERT: D  427 MET cc_start: 0.8793 (mmt) cc_final: 0.8538 (mmm)
REVERT: D  430 MET cc_start: 0.8490 (tmm) cc_final: 0.8187 (tmm)
REVERT: D  464 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8596 (tmm)
REVERT: D  657 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8378 (ptm)
  outliers start: 42
  outliers final: 33
  residues processed: 168
  average time/residue: 0.1248
  time to fit residues: 36.4231
Evaluate side-chains
  172 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 134
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  569 MET
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  464 MET
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  464 MET
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  569 MET
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  464 MET
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  657 MET
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 173 optimal weight:    2.9990
   chunk 211 optimal weight:    0.9990
   chunk 146 optimal weight:   20.0000
   chunk 86 optimal weight:    0.7980
   chunk 147 optimal weight:    0.0000
   chunk 152 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 212 optimal weight:    6.9990
   chunk 230 optimal weight:    8.9990
   chunk 208 optimal weight:    2.9990
   chunk 231 optimal weight:    0.8980
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.064026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.051087 restraints weight = 99025.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.052872 restraints weight = 54973.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.054137 restraints weight = 37244.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.054896 restraints weight = 28684.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055536 restraints weight = 24152.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055  24164  Z= 0.107
  Angle     :  0.490   7.620  32736  Z= 0.253
  Chirality :  0.037   0.196   3732
  Planarity :  0.004   0.039   4076
  Dihedral  :  5.895  59.998   3432
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.81 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.16), residues: 2880
  helix:  2.63 (0.11), residues: 2148
  sheet:  None (None), residues: 0
  loop : -0.60 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 330 
 TYR   0.009   0.001   TYR C  37 
 PHE   0.040   0.001   PHE D 568 
 TRP   0.021   0.001   TRP B 432 
 HIS   0.002   0.000   HIS A 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (24148)
  covalent geometry    : angle       0.48956 (32724)
  hydrogen bonds       : bond        0.03831 ( 1600)
  hydrogen bonds       : angle       3.37871 ( 4740)
  metal coordination   : bond        0.00189 (   16)
  metal coordination   : angle       0.96120 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 137
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 MET cc_start: 0.8726 (mmt) cc_final: 0.8481 (mmm)
REVERT: A  430 MET cc_start: 0.8496 (tmm) cc_final: 0.8187 (tmm)
REVERT: A  464 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8586 (tmm)
REVERT: B  427 MET cc_start: 0.9287 (mmp) cc_final: 0.8941 (mmm)
REVERT: B  430 MET cc_start: 0.8430 (tmm) cc_final: 0.8124 (tmm)
REVERT: B  464 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8579 (tmm)
REVERT: B  657 MET cc_start: 0.8568 (ptm) cc_final: 0.8346 (ptm)
REVERT: C  427 MET cc_start: 0.8730 (mmt) cc_final: 0.8477 (mmm)
REVERT: C  430 MET cc_start: 0.8494 (tmm) cc_final: 0.8184 (tmm)
REVERT: C  464 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8580 (tmm)
REVERT: D  427 MET cc_start: 0.8732 (mmt) cc_final: 0.8477 (mmm)
REVERT: D  430 MET cc_start: 0.8494 (tmm) cc_final: 0.8184 (tmm)
REVERT: D  464 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8589 (tmm)
REVERT: D  657 MET cc_start: 0.8572 (ptm) cc_final: 0.8302 (ptm)
  outliers start: 41
  outliers final: 30
  residues processed: 170
  average time/residue: 0.1310
  time to fit residues: 38.9081
Evaluate side-chains
  168 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  464 MET
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  464 MET
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  464 MET
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 174 optimal weight:    2.9990
   chunk 186 optimal weight:    6.9990
   chunk 283 optimal weight:    2.9990
   chunk 290 optimal weight:    0.9980
   chunk 159 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 234 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 596 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.062562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.049560 restraints weight = 99114.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.051280 restraints weight = 55575.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.052507 restraints weight = 38002.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.053355 restraints weight = 29460.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.053844 restraints weight = 24579.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.4416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  24164  Z= 0.153
  Angle     :  0.536   7.515  32736  Z= 0.280
  Chirality :  0.039   0.258   3732
  Planarity :  0.004   0.039   4076
  Dihedral  :  5.925  59.818   3432
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 13.36 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.16), residues: 2880
  helix:  2.50 (0.11), residues: 2176
  sheet:  None (None), residues: 0
  loop : -0.83 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 192 
 TYR   0.011   0.001   TYR D  37 
 PHE   0.039   0.002   PHE B 568 
 TRP   0.015   0.001   TRP B 432 
 HIS   0.003   0.001   HIS D 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (24148)
  covalent geometry    : angle       0.53518 (32724)
  hydrogen bonds       : bond        0.04262 ( 1600)
  hydrogen bonds       : angle       3.55955 ( 4740)
  metal coordination   : bond        0.00425 (   16)
  metal coordination   : angle       1.11444 (   12)

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

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

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5760 Ramachandran restraints generated.
    2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 MET cc_start: 0.8507 (tmm) cc_final: 0.8206 (tmm)
REVERT: A  464 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8633 (tmm)
REVERT: B  427 MET cc_start: 0.9225 (mmp) cc_final: 0.8754 (mmm)
REVERT: B  430 MET cc_start: 0.8307 (tmm) cc_final: 0.7975 (tmm)
REVERT: B  464 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8631 (tmm)
REVERT: B  657 MET cc_start: 0.8631 (ptm) cc_final: 0.8394 (ptm)
REVERT: C  169 MET cc_start: 0.8646 (mmm) cc_final: 0.8397 (mmm)
REVERT: C  430 MET cc_start: 0.8507 (tmm) cc_final: 0.8208 (tmm)
REVERT: C  464 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8628 (tmm)
REVERT: D   46 MET cc_start: 0.8769 (mtp) cc_final: 0.8547 (mtp)
REVERT: D  430 MET cc_start: 0.8509 (tmm) cc_final: 0.8206 (tmm)
REVERT: D  464 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8633 (tmm)
REVERT: D  657 MET cc_start: 0.8622 (ptm) cc_final: 0.8370 (ptm)
  outliers start: 37
  outliers final: 32
  residues processed: 161
  average time/residue: 0.1296
  time to fit residues: 36.3095
Evaluate side-chains
  163 residues out of total 2588 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  464 MET
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  515 ASP
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  464 MET
Chi-restraints excluded: chain B residue  489 VAL
Chi-restraints excluded: chain B residue  493 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  515 ASP
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 ILE
Chi-restraints excluded: chain C residue  464 MET
Chi-restraints excluded: chain C residue  489 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  795 ILE
Chi-restraints excluded: chain D residue  103 VAL
Chi-restraints excluded: chain D residue  464 MET
Chi-restraints excluded: chain D residue  489 VAL
Chi-restraints excluded: chain D residue  493 VAL
Chi-restraints excluded: chain D residue  502 THR
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  515 ASP
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  795 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 292
   random chunks:
   chunk 220 optimal weight:    4.9990
   chunk 227 optimal weight:   10.0000
   chunk 246 optimal weight:    3.9990
   chunk 226 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 75 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 148 optimal weight:    0.0010
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 ASN
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 659 ASN
** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.064008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.051053 restraints weight = 97735.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.052859 restraints weight = 53828.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.054047 restraints weight = 36438.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.054991 restraints weight = 27964.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.055525 restraints weight = 23149.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.4503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  24164  Z= 0.107
  Angle     :  0.522   8.285  32736  Z= 0.270
  Chirality :  0.037   0.221   3732
  Planarity :  0.004   0.040   4076
  Dihedral  :  5.921  59.931   3432
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 13.95 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.16), residues: 2880
  helix:  2.55 (0.11), residues: 2172
  sheet:  None (None), residues: 0
  loop : -0.84 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 202 
 TYR   0.010   0.001   TYR A 642 
 PHE   0.035   0.001   PHE C 568 
 TRP   0.017   0.001   TRP B 432 
 HIS   0.003   0.000   HIS B 377 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (24148)
  covalent geometry    : angle       0.52203 (32724)
  hydrogen bonds       : bond        0.03899 ( 1600)
  hydrogen bonds       : angle       3.43537 ( 4740)
  metal coordination   : bond        0.00146 (   16)
  metal coordination   : angle       0.81764 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2795.62 seconds
wall clock time: 49 minutes 41.22 seconds (2981.22 seconds total)