Starting phenix.real_space_refine
on Thu Feb 13 06:28:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kku_0703/02_2025/6kku_0703.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     S      68      5.16       5
     Cl      2      4.86       5
     C    5544      2.51       5
     N    1284      2.21       5
     O    1514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8412
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4068
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 26, 'TRANS': 510}
    Chain: "B"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4068
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 26, 'TRANS': 510}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "J"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'BGC': 1, 'GLC': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {' CL': 1, 'DU0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {' CL': 1, 'DU0': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.44, per 1000 atoms: 0.65
  Number of scatterers: 8412
  At special positions: 0
  Unit cell: (78.11, 101.65, 102.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      68     16.00
     O    1514      8.00
     N    1284      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 163 " - pdb=" SG  CYS A 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 343 " - pdb=" SG  CYS A 353 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 163 " - pdb=" SG  CYS B 626 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 308 " - pdb=" SG  CYS B 323 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 343 " - pdb=" SG  CYS B 353 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Links applied
    ALPHA1-4
      " BGC E   1 " - " GLC E   2 "
      " BGC F   1 " - " GLC F   2 "
      " BGC I   1 " - " GLC I   2 "
      " BGC J   1 " - " GLC J   2 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
    NAG-ASN
      " NAG C   1 " - " ASN A 312 "
      " NAG D   1 " - " ASN A 361 "
      " NAG G   1 " - " ASN B 312 "
      " NAG H   1 " - " ASN B 361 "
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.49
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      69.3% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
      removed outlier: 3.916A  pdb=" N   PHE A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 140
    Processing helix  chain 'A' and resid 141 through 176
      removed outlier: 7.212A  pdb=" N   VAL A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 8.871A  pdb=" N   LEU A 151 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   CYS A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS A 163 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   THR A 164 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 166 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 193
      removed outlier: 3.977A  pdb=" N   ILE A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 227
      removed outlier: 3.522A  pdb=" N   GLY A 198 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A 214 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 269
      removed outlier: 3.589A  pdb=" N   VAL A 253 " --> pdb=" O   ASN A 249 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR A 254 " --> pdb=" O   ASN A 250 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 266 " --> pdb=" O   MET A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 276
    Processing helix  chain 'A' and resid 278 through 298
    Processing helix  chain 'A' and resid 336 through 344
      removed outlier: 3.526A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.567A  pdb=" N   ASN A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 379
      removed outlier: 3.565A  pdb=" N   LEU A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.908A  pdb=" N   SER A 407 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
      removed outlier: 3.650A  pdb=" N   LEU A 423 " --> pdb=" O   SER A 419 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY A 425 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 431
      No H-bonds generated for 'chain 'A' and resid 429 through 431'
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 446 through 477
      removed outlier: 3.633A  pdb=" N   ILE A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
      Proline residue:  A 452  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE A 456 " --> pdb=" O   PRO A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.178A  pdb=" N   ASP A 488 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 500
    Processing helix  chain 'A' and resid 504 through 536
      Proline residue:  A 527  - end of helix
      removed outlier: 3.540A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 5.406A  pdb=" N   VAL A 544 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS A 547 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 570
      removed outlier: 3.895A  pdb=" N   LEU A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 602
      Proline residue:  A 579  - end of helix
      removed outlier: 3.751A  pdb=" N   GLN A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR A 600 " --> pdb=" O   CYS A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 634
      removed outlier: 3.741A  pdb=" N   SER A 619 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER A 634 " --> pdb=" O   MET A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 652
      removed outlier: 3.508A  pdb=" N   ALA A 638 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 133
      removed outlier: 3.916A  pdb=" N   PHE B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 140
    Processing helix  chain 'B' and resid 141 through 176
      removed outlier: 7.212A  pdb=" N   VAL B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 8.871A  pdb=" N   LEU B 151 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN B 152 " --> pdb=" O   ALA B 148 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   CYS B 162 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   CYS B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   THR B 164 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 166 " --> pdb=" O   CYS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 193
      removed outlier: 3.976A  pdb=" N   ILE B 189 " --> pdb=" O   SER B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 227
      removed outlier: 3.522A  pdb=" N   GLY B 198 " --> pdb=" O   GLY B 194 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ALA B 200 " --> pdb=" O   GLU B 196 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 214 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 269
      removed outlier: 3.589A  pdb=" N   VAL B 253 " --> pdb=" O   ASN B 249 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   TYR B 254 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LEU B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL B 266 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 276
    Processing helix  chain 'B' and resid 278 through 298
    Processing helix  chain 'B' and resid 336 through 344
      removed outlier: 3.526A  pdb=" N   PHE B 342 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.566A  pdb=" N   ASN B 360 " --> pdb=" O   TYR B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 379
      removed outlier: 3.566A  pdb=" N   LEU B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.908A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 428
      removed outlier: 3.649A  pdb=" N   LEU B 423 " --> pdb=" O   SER B 419 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY B 425 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 431
      No H-bonds generated for 'chain 'B' and resid 429 through 431'
    Processing helix  chain 'B' and resid 434 through 438
    Processing helix  chain 'B' and resid 446 through 477
      removed outlier: 3.632A  pdb=" N   ILE B 451 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
      Proline residue:  B 452  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE B 456 " --> pdb=" O   PRO B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 483
    Processing helix  chain 'B' and resid 484 through 488
      removed outlier: 4.179A  pdb=" N   ASP B 488 " --> pdb=" O   LYS B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 500
    Processing helix  chain 'B' and resid 504 through 536
      Proline residue:  B 527  - end of helix
      removed outlier: 3.539A  pdb=" N   ASP B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 547
      removed outlier: 5.405A  pdb=" N   VAL B 544 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS B 547 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 570
      removed outlier: 3.895A  pdb=" N   LEU B 559 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU B 567 " --> pdb=" O   LEU B 563 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 602
      Proline residue:  B 579  - end of helix
      removed outlier: 3.751A  pdb=" N   GLN B 599 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   THR B 600 " --> pdb=" O   CYS B 596 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 634
      removed outlier: 3.740A  pdb=" N   SER B 619 " --> pdb=" O   HIS B 615 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   SER B 634 " --> pdb=" O   MET B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 652
      removed outlier: 3.508A  pdb=" N   ALA B 638 " --> pdb=" O   SER B 634 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329
    Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329

    486 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2474
        1.35 -     1.47: 2313
        1.47 -     1.60: 3735
        1.60 -     1.72: 0
        1.72 -     1.85: 104
  Bond restraints: 8626
  Sorted by residual:
  bond pdb=" C5  GLC F   2 "
       pdb=" O5  GLC F   2 "
    ideal  model  delta    sigma   weight residual
    1.415  1.503 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C5  GLC I   2 "
       pdb=" O5  GLC I   2 "
    ideal  model  delta    sigma   weight residual
    1.415  1.503 -0.088 2.00e-02 2.50e+03 1.94e+01
  bond pdb=" C1  BGC E   1 "
       pdb=" O5  BGC E   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.494 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C1  BGC J   1 "
       pdb=" O5  BGC J   1 "
    ideal  model  delta    sigma   weight residual
    1.408  1.494 -0.086 2.00e-02 2.50e+03 1.85e+01
  bond pdb=" C1  GLC I   2 "
       pdb=" O5  GLC I   2 "
    ideal  model  delta    sigma   weight residual
    1.402  1.485 -0.083 2.00e-02 2.50e+03 1.71e+01
  ... (remaining 8621 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 11066
        1.95 -     3.89: 558
        3.89 -     5.84: 122
        5.84 -     7.79: 35
        7.79 -     9.73: 13
  Bond angle restraints: 11794
  Sorted by residual:
  angle pdb=" CA  PRO A 230 "
        pdb=" C   PRO A 230 "
        pdb=" N   PRO A 231 "
      ideal   model   delta    sigma   weight residual
     117.93  122.96   -5.03 1.20e+00 6.94e-01 1.75e+01
  angle pdb=" CA  PRO B 230 "
        pdb=" C   PRO B 230 "
        pdb=" N   PRO B 231 "
      ideal   model   delta    sigma   weight residual
     117.93  122.90   -4.97 1.20e+00 6.94e-01 1.72e+01
  angle pdb=" N   VAL A 490 "
        pdb=" CA  VAL A 490 "
        pdb=" C   VAL A 490 "
      ideal   model   delta    sigma   weight residual
     106.53  111.67   -5.14 1.41e+00 5.03e-01 1.33e+01
  angle pdb=" N   PHE A 428 "
        pdb=" CA  PHE A 428 "
        pdb=" C   PHE A 428 "
      ideal   model   delta    sigma   weight residual
     113.16  118.28   -5.12 1.42e+00 4.96e-01 1.30e+01
  angle pdb=" N   PHE B 428 "
        pdb=" CA  PHE B 428 "
        pdb=" C   PHE B 428 "
      ideal   model   delta    sigma   weight residual
     113.16  118.28   -5.12 1.42e+00 4.96e-01 1.30e+01
  ... (remaining 11789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.22: 5236
       34.22 -    68.43: 54
       68.43 -   102.65: 42
      102.65 -   136.86: 32
      136.86 -   171.08: 2
  Dihedral angle restraints: 5366
    sinusoidal: 2284
      harmonic: 3082
  Sorted by residual:
  dihedral pdb=" C26 DU0 A1106 "
           pdb=" C24 DU0 A1106 "
           pdb=" C25 DU0 A1106 "
           pdb=" O23 DU0 A1106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   18.24  171.08     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C26 DU0 B1108 "
           pdb=" C24 DU0 B1108 "
           pdb=" C25 DU0 B1108 "
           pdb=" O23 DU0 B1108 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   18.24  171.08     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" O2  GLC F   2 "
           pdb=" C2  GLC F   2 "
           pdb=" C3  GLC F   2 "
           pdb=" O3  GLC F   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.18 -167.16 -132.66     1      3.00e+01 1.11e-03 1.79e+01
  ... (remaining 5363 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1212
       0.080 -    0.160: 237
       0.160 -    0.240: 15
       0.240 -    0.319: 0
       0.319 -    0.399: 2
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B 312 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.80    0.40 2.00e-01 2.50e+01 3.98e+00
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 312 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.80    0.40 2.00e-01 2.50e+01 3.97e+00
  chirality pdb=" C1  GLC F   2 "
            pdb=" O4  BGC F   1 "
            pdb=" C2  GLC F   2 "
            pdb=" O5  GLC F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.37    0.03 2.00e-02 2.50e+03 1.68e+00
  ... (remaining 1463 not shown)

  Planarity restraints: 1408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 408 "   -0.048 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO B 409 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 409 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 409 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 408 "   -0.048 5.00e-02 4.00e+02   7.13e-02 8.12e+00
        pdb=" N   PRO A 409 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A 409 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 409 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 467 "   -0.016 2.00e-02 2.50e+03   1.66e-02 4.81e+00
        pdb=" CG  PHE A 467 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 467 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 467 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 467 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 467 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 467 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1405 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1782
        2.77 -     3.31: 7841
        3.31 -     3.84: 13265
        3.84 -     4.37: 14998
        4.37 -     4.90: 26580
  Nonbonded interactions: 64466
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 292 "
            pdb=" OG  SER A 468 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OH  TYR B 292 "
            pdb=" OG  SER B 468 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ILE A 169 "
            pdb=" OG  SER A 172 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   ILE B 169 "
            pdb=" OG  SER B 172 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O2  GLC F   2 "
            pdb=" O4  GLC F   2 "
     model   vdw
     2.383 3.040
  ... (remaining 64461 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.370
  Find NCS groups from input model:        0.340
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
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      :  0.009   0.088   8626  Z= 0.595
  Angle     :  1.082   9.734  11794  Z= 0.540
  Chirality :  0.061   0.399   1466
  Planarity :  0.008   0.071   1404
  Dihedral  : 18.283 171.079   3380
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.21), residues: 1070
  helix: -1.68 (0.16), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.97 (0.25), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 339 
 HIS   0.006   0.001   HIS B 615 
 PHE   0.039   0.004   PHE A 467 
 TYR   0.025   0.003   TYR A 292 
 ARG   0.004   0.001   ARG B 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.991 
Fit side-chains
REVERT: A  180 VAL cc_start: 0.8404 (t) cc_final: 0.8169 (t)
REVERT: A  297 LYS cc_start: 0.8588 (tttm) cc_final: 0.7946 (mmtm)
REVERT: A  405 LYS cc_start: 0.8370 (tttp) cc_final: 0.7862 (ttpp)
REVERT: B  144 MET cc_start: 0.8255 (ttm) cc_final: 0.7995 (ttt)
REVERT: B  176 THR cc_start: 0.8818 (p) cc_final: 0.8435 (t)
REVERT: B  297 LYS cc_start: 0.8699 (tttm) cc_final: 0.7868 (mmtm)
REVERT: B  405 LYS cc_start: 0.8357 (tttp) cc_final: 0.7864 (ttpp)
REVERT: B  484 ASP cc_start: 0.8380 (m-30) cc_final: 0.8071 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 293
  average time/residue: 0.2368
  time to fit residues: 92.0279
Evaluate side-chains
  141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 80 optimal weight:    0.3980
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0000
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 83 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 130 GLN
A 531 GLN
B 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.135260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.111455 restraints weight = 13616.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.114831 restraints weight = 7691.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116963 restraints weight = 5406.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8626  Z= 0.176
  Angle     :  0.695   8.586  11794  Z= 0.324
  Chirality :  0.043   0.207   1466
  Planarity :  0.005   0.065   1404
  Dihedral  : 14.599 149.555   1648
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  9.30 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1070
  helix:  0.59 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.57 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 616 
 HIS   0.002   0.001   HIS A 344 
 PHE   0.012   0.001   PHE B 467 
 TYR   0.018   0.001   TYR A 613 
 ARG   0.004   0.001   ARG A 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  289 LEU cc_start: 0.8672 (mm) cc_final: 0.8471 (mm)
REVERT: A  297 LYS cc_start: 0.8582 (tttm) cc_final: 0.7995 (mmtm)
REVERT: A  405 LYS cc_start: 0.8054 (tttp) cc_final: 0.7651 (ttpp)
REVERT: A  614 TYR cc_start: 0.7767 (t80) cc_final: 0.7208 (t80)
REVERT: B  130 GLN cc_start: 0.8031 (tt0) cc_final: 0.7680 (tt0)
REVERT: B  289 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (mm)
REVERT: B  297 LYS cc_start: 0.8721 (tttm) cc_final: 0.7897 (mmtm)
REVERT: B  380 LEU cc_start: 0.8759 (mt) cc_final: 0.8386 (mt)
REVERT: B  405 LYS cc_start: 0.7968 (tttp) cc_final: 0.7584 (ttpp)
REVERT: B  490 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7914 (p)
REVERT: B  537 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8065 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 194
  average time/residue: 0.1920
  time to fit residues: 53.6176
Evaluate side-chains
  154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  469 SER
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.2982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.133997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.109428 restraints weight = 13871.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.112741 restraints weight = 7827.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114914 restraints weight = 5537.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8626  Z= 0.209
  Angle     :  0.661  10.105  11794  Z= 0.318
  Chirality :  0.044   0.301   1466
  Planarity :  0.004   0.053   1404
  Dihedral  : 12.400 147.424   1648
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 11.90 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.25), residues: 1070
  helix:  1.32 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.30 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 616 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.027   0.001   PHE B 261 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.004   0.000   ARG B 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: A  405 LYS cc_start: 0.7991 (tttp) cc_final: 0.7607 (ttpp)
REVERT: B  130 GLN cc_start: 0.8065 (tt0) cc_final: 0.7727 (tt0)
REVERT: B  251 MET cc_start: 0.8655 (mmm) cc_final: 0.8405 (mtp)
REVERT: B  380 LEU cc_start: 0.8777 (mt) cc_final: 0.8510 (mt)
REVERT: B  392 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7902 (mt-10)
REVERT: B  405 LYS cc_start: 0.7926 (tttp) cc_final: 0.7560 (ttpp)
REVERT: B  410 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8441 (tt)
REVERT: B  537 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8199 (t0)
  outliers start: 21
  outliers final: 9
  residues processed: 169
  average time/residue: 0.1801
  time to fit residues: 43.3377
Evaluate side-chains
  145 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 91 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.5384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.133216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.108823 restraints weight = 13608.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112059 restraints weight = 7681.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.114184 restraints weight = 5459.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8626  Z= 0.221
  Angle     :  0.662   7.551  11794  Z= 0.314
  Chirality :  0.044   0.257   1466
  Planarity :  0.004   0.047   1404
  Dihedral  : 10.886 144.496   1648
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.81 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1070
  helix:  1.79 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.24 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 616 
 HIS   0.003   0.001   HIS A 615 
 PHE   0.014   0.001   PHE B 428 
 TYR   0.017   0.001   TYR B 613 
 ARG   0.002   0.000   ARG A 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: B  130 GLN cc_start: 0.8038 (tt0) cc_final: 0.7729 (tt0)
REVERT: B  380 LEU cc_start: 0.8759 (mt) cc_final: 0.8477 (mt)
REVERT: B  405 LYS cc_start: 0.7942 (tttp) cc_final: 0.7604 (ttpp)
REVERT: B  410 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8343 (tt)
  outliers start: 24
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1826
  time to fit residues: 41.7380
Evaluate side-chains
  150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 95 optimal weight:    9.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.111029 restraints weight = 13556.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.114324 restraints weight = 7686.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.116439 restraints weight = 5444.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8626  Z= 0.170
  Angle     :  0.641   8.724  11794  Z= 0.303
  Chirality :  0.043   0.231   1466
  Planarity :  0.004   0.041   1404
  Dihedral  :  9.747 140.481   1648
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.19 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.26), residues: 1070
  helix:  2.04 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.12 (0.26), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 616 
 HIS   0.001   0.000   HIS B 615 
 PHE   0.010   0.001   PHE B 428 
 TYR   0.014   0.001   TYR A 613 
 ARG   0.002   0.000   ARG A 492 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A  144 MET cc_start: 0.8139 (ttm) cc_final: 0.7790 (ttt)
REVERT: A  594 LEU cc_start: 0.9080 (tp) cc_final: 0.8813 (tp)
REVERT: B  130 GLN cc_start: 0.8013 (tt0) cc_final: 0.7669 (tt0)
REVERT: B  380 LEU cc_start: 0.8735 (mt) cc_final: 0.8468 (mt)
REVERT: B  405 LYS cc_start: 0.7870 (tttp) cc_final: 0.7529 (ttpp)
REVERT: B  410 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8466 (tt)
REVERT: B  594 LEU cc_start: 0.9053 (tp) cc_final: 0.8792 (tp)
REVERT: B  647 MET cc_start: 0.8412 (ttp) cc_final: 0.8209 (ttp)
  outliers start: 19
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1792
  time to fit residues: 42.0032
Evaluate side-chains
  146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  490 VAL
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    0.0270
   chunk 40 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 104 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0050
   overall best weight:    0.4652

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.112302 restraints weight = 13602.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.115666 restraints weight = 7774.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117768 restraints weight = 5519.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8626  Z= 0.162
  Angle     :  0.639   9.216  11794  Z= 0.301
  Chirality :  0.042   0.212   1466
  Planarity :  0.004   0.038   1404
  Dihedral  :  8.781 137.926   1648
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.08 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1070
  helix:  2.21 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.01 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 616 
 HIS   0.003   0.000   HIS B 615 
 PHE   0.010   0.001   PHE B 428 
 TYR   0.015   0.001   TYR A 613 
 ARG   0.003   0.000   ARG A 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLN cc_start: 0.7936 (tt0) cc_final: 0.7717 (tt0)
REVERT: A  144 MET cc_start: 0.8140 (ttm) cc_final: 0.7824 (ttt)
REVERT: A  405 LYS cc_start: 0.7895 (tttp) cc_final: 0.7540 (ttpp)
REVERT: A  594 LEU cc_start: 0.9059 (tp) cc_final: 0.8808 (tt)
REVERT: B  130 GLN cc_start: 0.7998 (tt0) cc_final: 0.7753 (tt0)
REVERT: B  380 LEU cc_start: 0.8708 (mt) cc_final: 0.8443 (mt)
REVERT: B  405 LYS cc_start: 0.7837 (tttp) cc_final: 0.7490 (ttpp)
REVERT: B  594 LEU cc_start: 0.9063 (tp) cc_final: 0.8818 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 172
  average time/residue: 0.1770
  time to fit residues: 43.5832
Evaluate side-chains
  154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 91 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0070
   chunk 68 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.6600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.136710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.112480 restraints weight = 13688.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.115769 restraints weight = 7786.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117862 restraints weight = 5542.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8626  Z= 0.176
  Angle     :  0.651   8.279  11794  Z= 0.307
  Chirality :  0.043   0.215   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  8.065 136.400   1648
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.67 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1070
  helix:  2.26 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.90 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 616 
 HIS   0.003   0.000   HIS B 615 
 PHE   0.011   0.001   PHE B 235 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   0.000   ARG A 317 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8136 (ttm) cc_final: 0.7827 (ttt)
REVERT: A  405 LYS cc_start: 0.7895 (tttp) cc_final: 0.7547 (ttpp)
REVERT: A  594 LEU cc_start: 0.9057 (tp) cc_final: 0.8805 (tt)
REVERT: B  130 GLN cc_start: 0.8019 (tt0) cc_final: 0.7756 (tt0)
REVERT: B  380 LEU cc_start: 0.8710 (mt) cc_final: 0.8442 (mt)
REVERT: B  405 LYS cc_start: 0.7847 (tttp) cc_final: 0.7499 (ttpp)
REVERT: B  594 LEU cc_start: 0.9067 (tp) cc_final: 0.8837 (tt)
  outliers start: 16
  outliers final: 15
  residues processed: 165
  average time/residue: 0.1846
  time to fit residues: 43.4529
Evaluate side-chains
  161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0070
   overall best weight:    0.6598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.137145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112968 restraints weight = 13790.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116325 restraints weight = 7823.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118420 restraints weight = 5552.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8626  Z= 0.175
  Angle     :  0.645   9.169  11794  Z= 0.305
  Chirality :  0.043   0.208   1466
  Planarity :  0.004   0.038   1404
  Dihedral  :  7.584 135.782   1648
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.33 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1070
  helix:  2.32 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.82 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 616 
 HIS   0.003   0.000   HIS B 615 
 PHE   0.011   0.001   PHE B 428 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 317 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8065 (ttm) cc_final: 0.7781 (ttt)
REVERT: A  405 LYS cc_start: 0.7848 (tttp) cc_final: 0.7488 (ttpp)
REVERT: A  594 LEU cc_start: 0.9046 (tp) cc_final: 0.8817 (tt)
REVERT: B  130 GLN cc_start: 0.8015 (tt0) cc_final: 0.7771 (tt0)
REVERT: B  380 LEU cc_start: 0.8704 (mt) cc_final: 0.8434 (mt)
REVERT: B  405 LYS cc_start: 0.7839 (tttp) cc_final: 0.7489 (ttpp)
REVERT: B  594 LEU cc_start: 0.9070 (tp) cc_final: 0.8854 (tt)
  outliers start: 17
  outliers final: 17
  residues processed: 158
  average time/residue: 0.1780
  time to fit residues: 40.3680
Evaluate side-chains
  159 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  521 GLN
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  521 GLN
Chi-restraints excluded: chain B residue  537 ASN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0470
   overall best weight:    1.8084

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.133698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109368 restraints weight = 13935.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.112648 restraints weight = 7954.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.114701 restraints weight = 5658.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8626  Z= 0.250
  Angle     :  0.685   8.965  11794  Z= 0.326
  Chirality :  0.045   0.233   1466
  Planarity :  0.004   0.041   1404
  Dihedral  :  7.411 137.815   1648
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.89 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1070
  helix:  2.11 (0.21), residues: 660
  sheet:  1.62 (1.12), residues: 20
  loop : -2.09 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS B 615 
 PHE   0.016   0.001   PHE B 428 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 140 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8099 (ttm) cc_final: 0.7790 (ttt)
REVERT: A  594 LEU cc_start: 0.9069 (tp) cc_final: 0.8835 (tt)
REVERT: B  380 LEU cc_start: 0.8801 (mt) cc_final: 0.8527 (mt)
REVERT: B  594 LEU cc_start: 0.9090 (tp) cc_final: 0.8857 (tt)
  outliers start: 18
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1824
  time to fit residues: 39.7449
Evaluate side-chains
  156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  521 GLN
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  131 ASN
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  521 GLN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0060
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9600

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.135414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111333 restraints weight = 13788.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114576 restraints weight = 7833.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.116691 restraints weight = 5581.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8626  Z= 0.192
  Angle     :  0.653   9.592  11794  Z= 0.312
  Chirality :  0.044   0.219   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  7.266 139.064   1648
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.12 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.26), residues: 1070
  helix:  2.24 (0.21), residues: 648
  sheet:  1.62 (1.12), residues: 20
  loop : -1.88 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 381 
 HIS   0.002   0.000   HIS B 615 
 PHE   0.011   0.001   PHE A 428 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 445 

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8077 (ttm) cc_final: 0.7745 (ttt)
REVERT: A  594 LEU cc_start: 0.9053 (tp) cc_final: 0.8841 (tt)
REVERT: B  380 LEU cc_start: 0.8777 (mt) cc_final: 0.8504 (mt)
REVERT: B  594 LEU cc_start: 0.9079 (tp) cc_final: 0.8879 (tt)
  outliers start: 16
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1862
  time to fit residues: 40.5703
Evaluate side-chains
  153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  600 THR
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  484 ASP
Chi-restraints excluded: chain B residue  521 GLN
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  581 LEU
Chi-restraints excluded: chain B residue  600 THR
Chi-restraints excluded: chain B residue  601 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0060
   chunk 55 optimal weight:    0.8980
   chunk 66 optimal weight:    0.1980
   chunk 76 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.113045 restraints weight = 13769.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.116326 restraints weight = 7912.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118396 restraints weight = 5640.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8626  Z= 0.168
  Angle     :  0.655  12.218  11794  Z= 0.312
  Chirality :  0.043   0.229   1466
  Planarity :  0.004   0.037   1404
  Dihedral  :  7.062 137.246   1648
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.14 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.27), residues: 1070
  helix:  2.36 (0.21), residues: 648
  sheet:  1.60 (1.15), residues: 20
  loop : -1.79 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 
 PHE   0.010   0.001   PHE B 428 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   0.000   ARG A 445 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2444.84 seconds
wall clock time: 44 minutes 47.86 seconds (2687.86 seconds total)