Starting phenix.real_space_refine
on Thu Mar 13 08:16:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kku_0703/03_2025/6kku_0703.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kku_0703/03_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_0703/03_2025/6kku_0703.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2025/6kku_0703.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_2025/6kku_0703.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kku_0703/03_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-5624/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: 5.64, per 1000 atoms: 0.67
  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: 2.68
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.84
  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: 2.24

  Time building geometry restraints manager: 3.01 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:             0.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.100
  Find NCS groups from input model:        0.360
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.800
-------------------------------------------------------------------------------
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  : 0.936 
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: 0.2254
  time to fit residues: 87.8529
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  : 0.967 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.111499 restraints weight = 13616.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.114844 restraints weight = 7664.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.117008 restraints weight = 5397.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
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  : 0.988 
Fit side-chains
REVERT: A  297 LYS cc_start: 0.8580 (tttm) cc_final: 0.7996 (mmtm)
REVERT: A  405 LYS cc_start: 0.8057 (tttp) cc_final: 0.7656 (ttpp)
REVERT: A  614 TYR cc_start: 0.7766 (t80) cc_final: 0.7209 (t80)
REVERT: B  130 GLN cc_start: 0.8030 (tt0) cc_final: 0.7681 (tt0)
REVERT: B  289 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8481 (mm)
REVERT: B  297 LYS cc_start: 0.8720 (tttm) cc_final: 0.7898 (mmtm)
REVERT: B  380 LEU cc_start: 0.8755 (mt) cc_final: 0.8385 (mt)
REVERT: B  405 LYS cc_start: 0.7971 (tttp) cc_final: 0.7588 (ttpp)
REVERT: B  490 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7916 (p)
REVERT: B  537 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8058 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 194
  average time/residue: 0.1703
  time to fit residues: 47.4786
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  : 0.923 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 28 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3630 r_free = 0.3630 target = 0.135226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.110717 restraints weight = 13830.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.114081 restraints weight = 7774.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116275 restraints weight = 5472.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8626  Z= 0.181
  Angle     :  0.650   9.719  11794  Z= 0.312
  Chirality :  0.044   0.284   1466
  Planarity :  0.004   0.052   1404
  Dihedral  : 12.286 147.002   1648
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.79 %
    Favored  : 85.94 %
  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: -0.05 (0.25), residues: 1070
  helix:  1.34 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.27 (0.27), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   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 A 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
  186 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 166
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: A  289 LEU cc_start: 0.8666 (mm) cc_final: 0.8462 (mm)
REVERT: A  297 LYS cc_start: 0.8600 (tttm) cc_final: 0.8011 (mmtm)
REVERT: A  405 LYS cc_start: 0.8015 (tttp) cc_final: 0.7641 (ttpp)
REVERT: B  130 GLN cc_start: 0.8028 (tt0) cc_final: 0.7692 (tt0)
REVERT: B  251 MET cc_start: 0.8630 (mmm) cc_final: 0.8368 (mtp)
REVERT: B  380 LEU cc_start: 0.8744 (mt) cc_final: 0.8481 (mt)
REVERT: B  392 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7894 (mt-10)
REVERT: B  405 LYS cc_start: 0.7905 (tttp) cc_final: 0.7566 (ttpp)
REVERT: B  410 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8386 (tt)
REVERT: B  537 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8177 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 178
  average time/residue: 0.1748
  time to fit residues: 44.4205
Evaluate side-chains
  150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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  602 LEU
Chi-restraints excluded: chain A residue  616 TRP
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:    0.7980
   chunk 91 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 23 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.134586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110097 restraints weight = 13612.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.113296 restraints weight = 7768.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115490 restraints weight = 5559.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3190

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= 0.201
  Angle     :  0.647   7.603  11794  Z= 0.306
  Chirality :  0.044   0.260   1466
  Planarity :  0.004   0.046   1404
  Dihedral  : 11.066 144.466   1648
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 12.81 %
    Favored  : 84.35 %
  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:  0.52 (0.26), residues: 1070
  helix:  1.91 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -2.22 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 616 
 HIS   0.004   0.001   HIS A 615 
 PHE   0.012   0.001   PHE B 428 
 TYR   0.017   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 492 

*********************** 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
  170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.8617 (mt) cc_final: 0.8290 (mt)
REVERT: B  130 GLN cc_start: 0.8007 (tt0) cc_final: 0.7690 (tt0)
REVERT: B  251 MET cc_start: 0.8612 (mmm) cc_final: 0.8404 (mtp)
REVERT: B  380 LEU cc_start: 0.8724 (mt) cc_final: 0.8443 (mt)
REVERT: B  405 LYS cc_start: 0.7920 (tttp) cc_final: 0.7567 (ttpp)
REVERT: B  410 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8497 (tt)
  outliers start: 25
  outliers final: 13
  residues processed: 162
  average time/residue: 0.1786
  time to fit residues: 41.6783
Evaluate side-chains
  147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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  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  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
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:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 25 optimal weight:    0.1980
   chunk 13 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.136004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.111718 restraints weight = 13699.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.115107 restraints weight = 7770.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.117260 restraints weight = 5499.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3418

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= 0.168
  Angle     :  0.628   8.747  11794  Z= 0.297
  Chirality :  0.043   0.232   1466
  Planarity :  0.004   0.040   1404
  Dihedral  :  9.994 139.619   1648
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.74 %
    Favored  : 82.88 %
  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:  0.80 (0.26), residues: 1070
  helix:  2.16 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.12 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 616 
 HIS   0.003   0.001   HIS A 615 
 PHE   0.010   0.001   PHE B 428 
 TYR   0.015   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 445 

*********************** 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
  175 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
REVERT: A  380 LEU cc_start: 0.8596 (mt) cc_final: 0.8388 (mt)
REVERT: A  405 LYS cc_start: 0.7966 (tttp) cc_final: 0.7587 (ttpp)
REVERT: A  416 ILE cc_start: 0.8711 (pt) cc_final: 0.8487 (pt)
REVERT: A  594 LEU cc_start: 0.9065 (tp) cc_final: 0.8800 (tp)
REVERT: B  130 GLN cc_start: 0.7972 (tt0) cc_final: 0.7690 (tt0)
REVERT: B  251 MET cc_start: 0.8568 (mmm) cc_final: 0.8304 (mtp)
REVERT: B  380 LEU cc_start: 0.8711 (mt) cc_final: 0.8469 (mt)
REVERT: B  405 LYS cc_start: 0.7848 (tttp) cc_final: 0.7502 (ttpp)
REVERT: B  594 LEU cc_start: 0.9050 (tp) cc_final: 0.8778 (tp)
  outliers start: 21
  outliers final: 11
  residues processed: 168
  average time/residue: 0.1789
  time to fit residues: 43.0968
Evaluate side-chains
  148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 137
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  600 THR
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 80 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0870
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.6758

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.136054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.111817 restraints weight = 13597.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115153 restraints weight = 7775.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.117294 restraints weight = 5529.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8626  Z= 0.171
  Angle     :  0.638   9.473  11794  Z= 0.299
  Chirality :  0.042   0.218   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  9.247 137.467   1648
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.87 %
    Favored  : 82.09 %
  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:  2.32 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop : -2.03 (0.26), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 616 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.013   0.001   PHE A 541 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.002   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
  169 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8085 (ttm) cc_final: 0.7777 (ttt)
REVERT: A  380 LEU cc_start: 0.8683 (mt) cc_final: 0.8272 (mt)
REVERT: A  405 LYS cc_start: 0.7946 (tttp) cc_final: 0.7573 (ttpp)
REVERT: A  416 ILE cc_start: 0.8708 (pt) cc_final: 0.8481 (pt)
REVERT: A  594 LEU cc_start: 0.9063 (tp) cc_final: 0.8808 (tt)
REVERT: B  130 GLN cc_start: 0.8034 (tt0) cc_final: 0.7752 (tt0)
REVERT: B  380 LEU cc_start: 0.8710 (mt) cc_final: 0.8440 (mt)
REVERT: B  405 LYS cc_start: 0.7883 (tttp) cc_final: 0.7530 (ttpp)
REVERT: B  594 LEU cc_start: 0.9063 (tp) cc_final: 0.8814 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 162
  average time/residue: 0.1805
  time to fit residues: 42.0021
Evaluate side-chains
  152 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  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  555 THR
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:    0.0010
   chunk 59 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.6588

-------------------------------------------------------------------------------
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 = 0.136698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.112405 restraints weight = 13706.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.115750 restraints weight = 7824.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.117884 restraints weight = 5563.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3714

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= 0.167
  Angle     :  0.630   8.903  11794  Z= 0.295
  Chirality :  0.042   0.215   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  8.506 135.783   1648
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.78 %
    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:  1.17 (0.26), residues: 1070
  helix:  2.39 (0.21), residues: 636
  sheet:  1.49 (1.12), residues: 20
  loop : -2.03 (0.27), residues: 414

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 A 428 
 TYR   0.015   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 445 

*********************** 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
  166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8134 (ttm) cc_final: 0.7826 (ttt)
REVERT: A  380 LEU cc_start: 0.8676 (mt) cc_final: 0.8259 (mt)
REVERT: A  405 LYS cc_start: 0.7929 (tttp) cc_final: 0.7566 (ttpp)
REVERT: A  416 ILE cc_start: 0.8696 (pt) cc_final: 0.8484 (pt)
REVERT: A  594 LEU cc_start: 0.9056 (tp) cc_final: 0.8804 (tt)
REVERT: B  130 GLN cc_start: 0.8013 (tt0) cc_final: 0.7745 (tt0)
REVERT: B  380 LEU cc_start: 0.8703 (mt) cc_final: 0.8434 (mt)
REVERT: B  405 LYS cc_start: 0.7856 (tttp) cc_final: 0.7505 (ttpp)
REVERT: B  594 LEU cc_start: 0.9059 (tp) cc_final: 0.8819 (tt)
  outliers start: 13
  outliers final: 13
  residues processed: 159
  average time/residue: 0.2138
  time to fit residues: 49.0195
Evaluate side-chains
  156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
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  538 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
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:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3625 r_free = 0.3625 target = 0.135270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.111071 restraints weight = 13789.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114414 restraints weight = 7838.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116534 restraints weight = 5547.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3766

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= 0.199
  Angle     :  0.647   9.073  11794  Z= 0.306
  Chirality :  0.043   0.221   1466
  Planarity :  0.004   0.039   1404
  Dihedral  :  7.950 136.010   1648
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.55 %
    Favored  : 81.63 %
  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:  1.15 (0.26), residues: 1070
  helix:  2.33 (0.21), residues: 648
  sheet:  1.64 (1.11), residues: 20
  loop : -2.09 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 616 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.013   0.001   PHE B 428 
 TYR   0.016   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 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
  161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8073 (ttm) cc_final: 0.7783 (ttt)
REVERT: A  380 LEU cc_start: 0.8715 (mt) cc_final: 0.8292 (mt)
REVERT: A  594 LEU cc_start: 0.9053 (tp) cc_final: 0.8818 (tt)
REVERT: B  130 GLN cc_start: 0.8037 (tt0) cc_final: 0.7765 (tt0)
REVERT: B  380 LEU cc_start: 0.8727 (mt) cc_final: 0.8455 (mt)
REVERT: B  405 LYS cc_start: 0.7815 (tttp) cc_final: 0.7486 (ttpp)
REVERT: B  410 LEU cc_start: 0.8829 (tp) cc_final: 0.8560 (tt)
REVERT: B  594 LEU cc_start: 0.9073 (tp) cc_final: 0.8849 (tt)
  outliers start: 16
  outliers final: 14
  residues processed: 153
  average time/residue: 0.1968
  time to fit residues: 43.4901
Evaluate side-chains
  151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
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  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  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  601 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0970
   chunk 100 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0470
   overall best weight:    0.5876

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.112421 restraints weight = 13860.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115762 restraints weight = 7893.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117863 restraints weight = 5605.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3879

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= 0.171
  Angle     :  0.650  12.810  11794  Z= 0.308
  Chirality :  0.043   0.214   1466
  Planarity :  0.004   0.037   1404
  Dihedral  :  7.486 135.779   1648
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.01 %
    Favored  : 81.41 %
  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:  1.27 (0.26), residues: 1070
  helix:  2.39 (0.21), residues: 648
  sheet:  1.59 (1.12), residues: 20
  loop : -1.97 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 
 PHE   0.010   0.001   PHE A 541 
 TYR   0.015   0.001   TYR B 613 
 ARG   0.002   0.000   ARG B 317 

*********************** 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
  163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 149
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8048 (ttm) cc_final: 0.7762 (ttt)
REVERT: A  380 LEU cc_start: 0.8740 (mt) cc_final: 0.8448 (mt)
REVERT: A  405 LYS cc_start: 0.7846 (tttp) cc_final: 0.7480 (ttpp)
REVERT: A  630 MET cc_start: 0.7901 (ttm) cc_final: 0.7650 (ttp)
REVERT: B  130 GLN cc_start: 0.7974 (tt0) cc_final: 0.7747 (tt0)
REVERT: B  380 LEU cc_start: 0.8741 (mt) cc_final: 0.8466 (mt)
REVERT: B  405 LYS cc_start: 0.7799 (tttp) cc_final: 0.7449 (ttpp)
REVERT: B  594 LEU cc_start: 0.9064 (tp) cc_final: 0.8853 (tt)
  outliers start: 14
  outliers final: 12
  residues processed: 156
  average time/residue: 0.2184
  time to fit residues: 49.7707
Evaluate side-chains
  155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
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  538 ILE
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  581 LEU
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:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0000
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9992

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.136112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.111870 restraints weight = 13787.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.115205 restraints weight = 7868.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.117315 restraints weight = 5593.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3934

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= 0.189
  Angle     :  0.671  11.809  11794  Z= 0.315
  Chirality :  0.044   0.216   1466
  Planarity :  0.004   0.038   1404
  Dihedral  :  7.212 136.004   1648
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 17.12 %
    Favored  : 81.41 %
  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:  1.32 (0.26), residues: 1070
  helix:  2.40 (0.21), residues: 648
  sheet:  1.61 (1.14), residues: 20
  loop : -1.89 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 381 
 HIS   0.003   0.001   HIS B 615 
 PHE   0.012   0.001   PHE B 428 
 TYR   0.015   0.001   TYR B 613 
 ARG   0.001   0.000   ARG A 191 

********************** 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
  157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 1.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8077 (ttm) cc_final: 0.7792 (ttt)
REVERT: A  380 LEU cc_start: 0.8767 (mt) cc_final: 0.8472 (mt)
REVERT: B  130 GLN cc_start: 0.8004 (tt0) cc_final: 0.7780 (tt0)
REVERT: B  380 LEU cc_start: 0.8750 (mt) cc_final: 0.8465 (mt)
REVERT: B  405 LYS cc_start: 0.7790 (tttp) cc_final: 0.7477 (ttpp)
REVERT: B  594 LEU cc_start: 0.9057 (tp) cc_final: 0.8847 (tt)
  outliers start: 13
  outliers final: 13
  residues processed: 151
  average time/residue: 0.2668
  time to fit residues: 58.6961
Evaluate side-chains
  155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  193 LEU
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  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  538 ILE
Chi-restraints excluded: chain B residue  581 LEU
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:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 22 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0870
   chunk 55 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0060
   chunk 76 optimal weight:    0.0040
   chunk 46 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.2786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.138523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.114593 restraints weight = 13817.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117982 restraints weight = 7824.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.120150 restraints weight = 5517.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.4132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8626  Z= 0.157
  Angle     :  0.645  11.315  11794  Z= 0.304
  Chirality :  0.042   0.213   1466
  Planarity :  0.004   0.036   1404
  Dihedral  :  7.031 134.609   1648
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 17.46 %
    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:  1.44 (0.27), residues: 1070
  helix:  2.45 (0.21), residues: 650
  sheet:  1.38 (1.16), residues: 20
  loop : -1.75 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 616 
 HIS   0.002   0.000   HIS B 615 
 PHE   0.010   0.001   PHE A 541 
 TYR   0.015   0.001   TYR B 613 
 ARG   0.003   0.000   ARG A 445 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2638.65 seconds
wall clock time: 48 minutes 5.35 seconds (2885.35 seconds total)