Starting phenix.real_space_refine
on Sat Oct 11 02:15:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k53_36896/10_2025/8k53_36896.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    6663      2.51       5
     N    1852      2.21       5
     O    2043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10602
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5998
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 777, 5998
          Classifications: {'peptide': 777}
          Link IDs: {'PCIS': 8, 'PTRANS': 48, 'TRANS': 720}
    Chain: "B"
      Number of atoms: 4439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4439
          Classifications: {'peptide': 573}
          Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    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: 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: "F"
      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: "A"
      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: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.24, per 1000 atoms: 0.21
  Number of scatterers: 10602
  At special positions: 0
  Unit cell: (106.72, 168.36, 207.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    2043      8.00
     N    1852      7.00
     C    6663      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 261 " - pdb=" SG  CYS A 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 440 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 111 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 261 " - pdb=" SG  CYS B 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 348 " - pdb=" SG  CYS B 395 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 440 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 587 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A1101 " - " ASN A  76 "
      " NAG A1102 " - " ASN A 477 "
      " NAG B1101 " - " ASN B  76 "
      " NAG C   1 " - " ASN A 461 "
      " NAG D   1 " - " ASN A 498 "
      " NAG E   1 " - " ASN B 461 "
      " NAG F   1 " - " ASN B 498 "
  Time building additional restraints: 1.19
  Conformation dependent library (CDL) restraints added in 534.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2490

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 44 sheets defined
      3.0% alpha, 47.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 198 through 202
      removed outlier: 3.684A  pdb=" N   LEU A 202 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 301
      removed outlier: 3.863A  pdb=" N   GLU A 301 " --> pdb=" O   PHE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.739A  pdb=" N   ASP A 482 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLU A 483 " --> pdb=" O   ARG A 480 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 479 through 483'
    Processing helix  chain 'B' and resid 101 through 106
      removed outlier: 4.118A  pdb=" N   ALA B 106 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.616A  pdb=" N   LEU B 202 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 301
      removed outlier: 3.845A  pdb=" N   GLU B 301 " --> pdb=" O   PHE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 3.596A  pdb=" N   GLU B 483 " --> pdb=" O   ARG B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 582
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41
      removed outlier: 5.690A  pdb=" N   GLY A  36 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   SER A  66 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ARG A  62 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49
      removed outlier: 6.297A  pdb=" N   VAL A  46 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   GLY A 130 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   PHE A  48 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   LEU A 132 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79
    Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59
    Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 145
      removed outlier: 6.277A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY A 203 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 145
      removed outlier: 6.277A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY A 203 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 153
    Processing sheet with id=AA8, first strand: chain 'A' and resid 237 through 243
      removed outlier: 5.682A  pdb=" N   ALA A 238 " --> pdb=" O   ASN A 266 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   ASN A 266 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   PHE A 262 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252
      removed outlier: 6.471A  pdb=" N   THR A 249 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   GLN A 324 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260
    Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331
      removed outlier: 6.457A  pdb=" N   ALA A 349 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339
    Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 347
    Processing sheet with id=AB5, first strand: chain 'A' and resid 430 through 431
      removed outlier: 6.863A  pdb=" N   ALA A 430 " --> pdb=" O   ARG A 506 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB5
    Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 438
    Processing sheet with id=AB7, first strand: chain 'A' and resid 457 through 458
    Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513
      removed outlier: 6.311A  pdb=" N   HIS A 531 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 520
      removed outlier: 3.615A  pdb=" N   VAL A 602 " --> pdb=" O   GLY A 583 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY A 583 " --> pdb=" O   VAL A 602 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528
      removed outlier: 3.687A  pdb=" N   LEU A 526 " --> pdb=" O   ILE A 574 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 612 through 617
      removed outlier: 3.621A  pdb=" N   GLY A 612 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   VAL A 614 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 627 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   VAL A 616 " --> pdb=" O   GLN A 625 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   GLN A 625 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 654 through 655
      removed outlier: 6.311A  pdb=" N   VAL A 685 " --> pdb=" O   PRO A 696 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 694 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 663 through 664
      removed outlier: 4.671A  pdb=" N   ILE A 663 " --> pdb=" O   TYR A 641 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE A 703 " --> pdb=" O   TYR A 681 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 718 through 719
    Processing sheet with id=AC6, first strand: chain 'A' and resid 759 through 764
      removed outlier: 6.437A  pdb=" N   ILE A 788 " --> pdb=" O   GLU A 799 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   GLU A 799 " --> pdb=" O   ILE A 788 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   SER A 790 " --> pdb=" O   GLY A 797 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 759 through 764
    Processing sheet with id=AC8, first strand: chain 'B' and resid 35 through 41
      removed outlier: 5.948A  pdb=" N   GLY B  36 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   SER B  66 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ARG B  62 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 46 through 49
      removed outlier: 6.275A  pdb=" N   VAL B  46 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   GLY B 130 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   PHE B  48 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 8.795A  pdb=" N   LEU B 132 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 78 through 79
      removed outlier: 3.504A  pdb=" N   THR B  78 " --> pdb=" O   MET B  75 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 56 through 59
      removed outlier: 3.664A  pdb=" N   VAL B  96 " --> pdb=" O   GLN B  89 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 143 through 144
      removed outlier: 6.063A  pdb=" N   VAL B 143 " --> pdb=" O   ASN B 228 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY B 203 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 143 through 144
      removed outlier: 6.063A  pdb=" N   VAL B 143 " --> pdb=" O   ASN B 228 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY B 203 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 151 through 153
    Processing sheet with id=AD6, first strand: chain 'B' and resid 237 through 243
      removed outlier: 5.571A  pdb=" N   ALA B 238 " --> pdb=" O   ASN B 266 " (cutoff:3.500A)
      removed outlier: 5.470A  pdb=" N   ASN B 266 " --> pdb=" O   ALA B 238 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   PHE B 262 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 248 through 252
      removed outlier: 3.689A  pdb=" N   ILE B 322 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'B' and resid 248 through 252
      removed outlier: 3.689A  pdb=" N   ILE B 322 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLN B 326 " --> pdb=" O   LYS B 353 " (cutoff:3.500A)
      removed outlier: 5.126A  pdb=" N   LYS B 353 " --> pdb=" O   GLN B 326 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA B 349 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'B' and resid 257 through 260
    Processing sheet with id=AE1, first strand: chain 'B' and resid 336 through 339
      removed outlier: 6.491A  pdb=" N   THR B 336 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   GLN B 413 " --> pdb=" O   THR B 336 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ALA B 338 " --> pdb=" O   GLN B 413 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'B' and resid 343 through 347
    Processing sheet with id=AE3, first strand: chain 'B' and resid 415 through 418
      removed outlier: 5.513A  pdb=" N   ALA B 416 " --> pdb=" O   ALA B 445 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   ALA B 445 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'B' and resid 427 through 431
      removed outlier: 7.016A  pdb=" N   ILE B 428 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   ARG B 506 " --> pdb=" O   ILE B 428 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   ALA B 430 " --> pdb=" O   ARG B 506 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'B' and resid 436 through 438
    Processing sheet with id=AE6, first strand: chain 'B' and resid 510 through 513
      removed outlier: 6.196A  pdb=" N   HIS B 531 " --> pdb=" O   THR B 512 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'B' and resid 518 through 521
    Processing sheet with id=AE8, first strand: chain 'B' and resid 526 through 528

    391 hydrogen bonds defined for protein.
    906 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: 2.46

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3525
        1.34 -     1.46: 2407
        1.46 -     1.58: 4858
        1.58 -     1.70: 0
        1.70 -     1.82: 64
  Bond restraints: 10854
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.464 -0.058 2.00e-02 2.50e+03 8.31e+00
  bond pdb=" C1  NAG A1102 "
       pdb=" O5  NAG A1102 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.78e+00
  bond pdb=" C1  BMA C   3 "
       pdb=" C2  BMA C   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.557 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" CB  PRO B 469 "
       pdb=" CG  PRO B 469 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.56e+00
  bond pdb=" C1  NAG B1101 "
       pdb=" O5  NAG B1101 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.13e+00
  ... (remaining 10849 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 14382
        1.67 -     3.35: 338
        3.35 -     5.02: 33
        5.02 -     6.69: 16
        6.69 -     8.36: 6
  Bond angle restraints: 14775
  Sorted by residual:
  angle pdb=" CA  PRO B 469 "
        pdb=" N   PRO B 469 "
        pdb=" CD  PRO B 469 "
      ideal   model   delta    sigma   weight residual
     112.00  104.14    7.86 1.40e+00 5.10e-01 3.15e+01
  angle pdb=" C   ASN A 498 "
        pdb=" CA  ASN A 498 "
        pdb=" CB  ASN A 498 "
      ideal   model   delta    sigma   weight residual
     109.72  115.30   -5.58 1.61e+00 3.86e-01 1.20e+01
  angle pdb=" CA  GLN B 318 "
        pdb=" CB  GLN B 318 "
        pdb=" CG  GLN B 318 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  angle pdb=" CB  GLN B 318 "
        pdb=" CG  GLN B 318 "
        pdb=" CD  GLN B 318 "
      ideal   model   delta    sigma   weight residual
     112.60  118.19   -5.59 1.70e+00 3.46e-01 1.08e+01
  angle pdb=" C   SER B  86 "
        pdb=" N   ARG B  87 "
        pdb=" CA  ARG B  87 "
      ideal   model   delta    sigma   weight residual
     120.99  127.11   -6.12 1.86e+00 2.89e-01 1.08e+01
  ... (remaining 14770 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.45: 6193
       21.45 -    42.90: 415
       42.90 -    64.35: 78
       64.35 -    85.81: 17
       85.81 -   107.26: 6
  Dihedral angle restraints: 6709
    sinusoidal: 2836
      harmonic: 3873
  Sorted by residual:
  dihedral pdb=" CA  ALA A 497 "
           pdb=" C   ALA A 497 "
           pdb=" N   ASN A 498 "
           pdb=" CA  ASN A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.08  -20.92     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  TRP A 678 "
           pdb=" C   TRP A 678 "
           pdb=" N   MET A 679 "
           pdb=" CA  MET A 679 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" O4  BMA C   3 "
           pdb=" C4  BMA C   3 "
           pdb=" C5  BMA C   3 "
           pdb=" O5  BMA C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.55  107.26     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 6706 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1657
       0.151 -    0.301: 7
       0.301 -    0.452: 1
       0.452 -    0.603: 0
       0.603 -    0.753: 1
  Chirality restraints: 1666
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 461 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.65   -0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 498 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.81    0.41 2.00e-01 2.50e+01 4.12e+00
  chirality pdb=" C5  BMA C   3 "
            pdb=" C4  BMA C   3 "
            pdb=" C6  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.26 2.00e-01 2.50e+01 1.71e+00
  ... (remaining 1663 not shown)

  Planarity restraints: 1937
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 468 "   -0.071 5.00e-02 4.00e+02   1.03e-01 1.71e+01
        pdb=" N   PRO B 469 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO B 469 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 469 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 498 "    0.038 2.00e-02 2.50e+03   3.51e-02 1.54e+01
        pdb=" CG  ASN A 498 "   -0.047 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 498 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 498 "   -0.034 2.00e-02 2.50e+03
        pdb=" C1  NAG D   1 "    0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 498 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" CG  ASN A 498 "   -0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 498 "    0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 498 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1934 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 313
        2.70 -     3.25: 9310
        3.25 -     3.80: 15472
        3.80 -     4.35: 19189
        4.35 -     4.90: 33322
  Nonbonded interactions: 77606
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 218 "
            pdb=" O   SER B 219 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" N   GLU B  55 "
            pdb=" OE1 GLU B  55 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OG  SER A 165 "
            pdb=" OG1 THR A 210 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG A 464 "
            pdb=" OD2 ASP A 482 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" NH2 ARG A 355 "
            pdb=" O   MET B 538 "
     model   vdw
     2.295 3.120
  ... (remaining 77601 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             5.720
  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:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.020
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
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      :  0.003   0.080  10878  Z= 0.148
  Angle     :  0.693  18.534  14835  Z= 0.334
  Chirality :  0.049   0.753   1666
  Planarity :  0.005   0.103   1930
  Dihedral  : 15.218 107.256   4183
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.75 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 17.13 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.23), residues: 1346
  helix:  None (None), residues: 0
  sheet:  0.86 (0.20), residues: 657
  loop : -0.82 (0.23), residues: 689

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 506 
 TYR   0.014   0.001   TYR B 166 
 PHE   0.022   0.001   PHE A 173 
 TRP   0.007   0.001   TRP A  73 
 HIS   0.008   0.001   HIS B 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10854)
  covalent geometry    : angle       0.62542 (14775)
  SS BOND              : bond        0.00189 (   12)
  SS BOND              : angle       0.44012 (   24)
  hydrogen bonds       : bond        0.10743 (  352)
  hydrogen bonds       : angle       5.67333 (  906)
  link_BETA1-4         : bond        0.00578 (    5)
  link_BETA1-4         : angle       3.09671 (   15)
  link_NAG-ASN         : bond        0.01058 (    7)
  link_NAG-ASN         : angle       7.51686 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 0.411 
Fit side-chains
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.1102
  time to fit residues: 9.5336
Evaluate side-chains
  54 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain B residue  306 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0570
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0770
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 HIS
B 146 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.193471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.174649 restraints weight = 17682.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.169775 restraints weight = 26223.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.167010 restraints weight = 31022.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.166096 restraints weight = 35195.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.164165 restraints weight = 27293.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.0583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10878  Z= 0.113
  Angle     :  0.614  17.256  14835  Z= 0.296
  Chirality :  0.046   0.623   1666
  Planarity :  0.004   0.066   1930
  Dihedral  :  7.397  65.286   1721
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  5.13 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.71 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.23), residues: 1346
  helix: -5.40 (0.24), residues: 6
  sheet:  0.88 (0.20), residues: 656
  loop : -0.84 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 244 
 TYR   0.009   0.001   TYR B 405 
 PHE   0.028   0.002   PHE B 184 
 TRP   0.008   0.001   TRP A 149 
 HIS   0.006   0.001   HIS B 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10854)
  covalent geometry    : angle       0.55864 (14775)
  SS BOND              : bond        0.00181 (   12)
  SS BOND              : angle       0.44351 (   24)
  hydrogen bonds       : bond        0.02757 (  352)
  hydrogen bonds       : angle       5.04745 (  906)
  link_BETA1-4         : bond        0.00689 (    5)
  link_BETA1-4         : angle       2.52407 (   15)
  link_NAG-ASN         : bond        0.01143 (    7)
  link_NAG-ASN         : angle       6.45004 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 61
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7511 (ppp) cc_final: 0.6982 (ppp)
REVERT: A  468 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8253 (m)
REVERT: B  152 MET cc_start: 0.6969 (tmm) cc_final: 0.5928 (ttt)
  outliers start: 28
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0949
  time to fit residues: 11.5206
Evaluate side-chains
  72 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  421 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 106 optimal weight:    0.4980
   chunk 52 optimal weight:    7.9990
   chunk 62 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 130 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 67 optimal weight:   20.0000
   chunk 4 optimal weight:    0.7980
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** 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 = 0.4259 r_free = 0.4259 target = 0.185083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.163479 restraints weight = 17841.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.159544 restraints weight = 36456.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.158139 restraints weight = 37907.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156788 restraints weight = 35799.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.155356 restraints weight = 31910.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7063
moved from start:          0.1369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.075  10878  Z= 0.311
  Angle     :  0.769  17.349  14835  Z= 0.384
  Chirality :  0.051   0.667   1666
  Planarity :  0.006   0.070   1930
  Dihedral  :  7.010  58.638   1720
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.39 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.42 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1346
  helix:  None (None), residues: 0
  sheet:  0.71 (0.20), residues: 627
  loop : -1.18 (0.22), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 464 
 TYR   0.023   0.002   TYR A 109 
 PHE   0.030   0.002   PHE B 184 
 TRP   0.017   0.002   TRP B 346 
 HIS   0.004   0.001   HIS B 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.00769 (10854)
  covalent geometry    : angle       0.72911 (14775)
  SS BOND              : bond        0.00298 (   12)
  SS BOND              : angle       1.06995 (   24)
  hydrogen bonds       : bond        0.04305 (  352)
  hydrogen bonds       : angle       5.58907 (  906)
  link_BETA1-4         : bond        0.00494 (    5)
  link_BETA1-4         : angle       2.43806 (   15)
  link_NAG-ASN         : bond        0.00875 (    7)
  link_NAG-ASN         : angle       6.20208 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 61
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A   98 MET cc_start: 0.7668 (ppp) cc_final: 0.7175 (ppp)
REVERT: A  427 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8469 (mt)
  outliers start: 40
  outliers final: 27
  residues processed: 95
  average time/residue: 0.0884
  time to fit residues: 12.6267
Evaluate side-chains
  84 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 56
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  221 PHE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  467 VAL
Chi-restraints excluded: chain B residue  592 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   chunk 128 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 183 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.191153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.170645 restraints weight = 17618.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.166672 restraints weight = 34486.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.164778 restraints weight = 36599.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.164765 restraints weight = 38691.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.164356 restraints weight = 24876.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10878  Z= 0.130
  Angle     :  0.625  16.454  14835  Z= 0.305
  Chirality :  0.046   0.621   1666
  Planarity :  0.004   0.070   1930
  Dihedral  :  6.138  56.363   1720
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.16 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.77 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.23), residues: 1346
  helix: -5.44 (0.23), residues: 6
  sheet:  0.78 (0.20), residues: 628
  loop : -1.02 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 789 
 TYR   0.011   0.001   TYR B 405 
 PHE   0.029   0.002   PHE A 493 
 TRP   0.022   0.001   TRP A 273 
 HIS   0.006   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10854)
  covalent geometry    : angle       0.58539 (14775)
  SS BOND              : bond        0.00202 (   12)
  SS BOND              : angle       0.50194 (   24)
  hydrogen bonds       : bond        0.02892 (  352)
  hydrogen bonds       : angle       5.07794 (  906)
  link_BETA1-4         : bond        0.00424 (    5)
  link_BETA1-4         : angle       2.30943 (   15)
  link_NAG-ASN         : bond        0.00922 (    7)
  link_NAG-ASN         : angle       5.56863 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 66
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7584 (ppp) cc_final: 0.7224 (ppp)
REVERT: A  135 PHE cc_start: 0.6400 (OUTLIER) cc_final: 0.5971 (m-10)
REVERT: A  355 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7986 (mpt180)
REVERT: A  468 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8375 (m)
REVERT: A  789 ARG cc_start: -0.1400 (OUTLIER) cc_final: -0.2337 (tmt170)
REVERT: B  233 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.5380 (p0)
  outliers start: 39
  outliers final: 28
  residues processed: 96
  average time/residue: 0.0968
  time to fit residues: 13.8552
Evaluate side-chains
  91 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.187849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.166459 restraints weight = 17636.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.161785 restraints weight = 34793.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.160082 restraints weight = 36204.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.158808 restraints weight = 38211.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.157014 restraints weight = 32740.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10878  Z= 0.150
  Angle     :  0.621  16.079  14835  Z= 0.305
  Chirality :  0.046   0.628   1666
  Planarity :  0.005   0.076   1930
  Dihedral  :  5.747  54.674   1718
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.57 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.13 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.23), residues: 1346
  helix: -5.43 (0.23), residues: 6
  sheet:  0.80 (0.20), residues: 628
  loop : -0.99 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 789 
 TYR   0.011   0.001   TYR B 405 
 PHE   0.028   0.002   PHE A 493 
 TRP   0.012   0.001   TRP A 149 
 HIS   0.004   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (10854)
  covalent geometry    : angle       0.58439 (14775)
  SS BOND              : bond        0.00211 (   12)
  SS BOND              : angle       0.55770 (   24)
  hydrogen bonds       : bond        0.02978 (  352)
  hydrogen bonds       : angle       4.99097 (  906)
  link_BETA1-4         : bond        0.00444 (    5)
  link_BETA1-4         : angle       2.23292 (   15)
  link_NAG-ASN         : bond        0.00834 (    7)
  link_NAG-ASN         : angle       5.32689 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 60
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7606 (ppp) cc_final: 0.7399 (ppp)
REVERT: A  135 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6145 (m-10)
REVERT: A  355 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8002 (mpt180)
REVERT: A  468 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8416 (m)
REVERT: A  562 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7103 (ttt180)
REVERT: A  679 MET cc_start: 0.1785 (mpp) cc_final: 0.1413 (tpt)
REVERT: A  789 ARG cc_start: -0.1297 (OUTLIER) cc_final: -0.2261 (tmt170)
  outliers start: 46
  outliers final: 33
  residues processed: 99
  average time/residue: 0.0968
  time to fit residues: 14.4579
Evaluate side-chains
  94 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 56
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  211 SER
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 116 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:   10.0000
   chunk 98 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 71 optimal weight:   50.0000
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 HIS ** 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 = 0.4261 r_free = 0.4261 target = 0.185309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.164472 restraints weight = 17646.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.159255 restraints weight = 33906.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.157311 restraints weight = 37954.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156845 restraints weight = 36231.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.155293 restraints weight = 28417.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  10878  Z= 0.244
  Angle     :  0.700  16.341  14835  Z= 0.347
  Chirality :  0.048   0.650   1666
  Planarity :  0.005   0.074   1930
  Dihedral  :  6.006  56.351   1718
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.09 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 16.86 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.22), residues: 1346
  helix: -5.45 (0.23), residues: 6
  sheet:  0.73 (0.20), residues: 627
  loop : -1.11 (0.22), residues: 713

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 420 
 TYR   0.020   0.002   TYR A 109 
 PHE   0.030   0.002   PHE A 493 
 TRP   0.033   0.002   TRP A 273 
 HIS   0.003   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (10854)
  covalent geometry    : angle       0.66618 (14775)
  SS BOND              : bond        0.00265 (   12)
  SS BOND              : angle       0.85334 (   24)
  hydrogen bonds       : bond        0.03754 (  352)
  hydrogen bonds       : angle       5.30121 (  906)
  link_BETA1-4         : bond        0.00442 (    5)
  link_BETA1-4         : angle       2.30109 (   15)
  link_NAG-ASN         : bond        0.00795 (    7)
  link_NAG-ASN         : angle       5.37968 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 59
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6402 (m-10)
REVERT: A  346 TRP cc_start: 0.9235 (OUTLIER) cc_final: 0.8012 (m-10)
REVERT: A  468 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8467 (m)
REVERT: A  562 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7049 (ttt180)
REVERT: A  679 MET cc_start: 0.1657 (mpp) cc_final: 0.1247 (tpt)
REVERT: A  789 ARG cc_start: -0.1151 (OUTLIER) cc_final: -0.2124 (tmt170)
  outliers start: 57
  outliers final: 37
  residues processed: 111
  average time/residue: 0.0915
  time to fit residues: 15.6823
Evaluate side-chains
  98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 56
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 133 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 HIS ** 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 = 0.4279 r_free = 0.4279 target = 0.186862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.165823 restraints weight = 17448.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.161243 restraints weight = 32249.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.159054 restraints weight = 32255.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.158302 restraints weight = 36637.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.157195 restraints weight = 27163.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10878  Z= 0.169
  Angle     :  0.661  15.927  14835  Z= 0.322
  Chirality :  0.046   0.625   1666
  Planarity :  0.005   0.078   1930
  Dihedral  :  5.726  54.907   1718
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.65 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.28 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.22), residues: 1346
  helix: -5.45 (0.23), residues: 6
  sheet:  0.74 (0.20), residues: 632
  loop : -1.04 (0.23), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 425 
 TYR   0.012   0.001   TYR B 405 
 PHE   0.030   0.002   PHE A 493 
 TRP   0.026   0.001   TRP A 273 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10854)
  covalent geometry    : angle       0.62790 (14775)
  SS BOND              : bond        0.00216 (   12)
  SS BOND              : angle       0.65938 (   24)
  hydrogen bonds       : bond        0.03192 (  352)
  hydrogen bonds       : angle       5.10826 (  906)
  link_BETA1-4         : bond        0.00422 (    5)
  link_BETA1-4         : angle       2.28785 (   15)
  link_NAG-ASN         : bond        0.00792 (    7)
  link_NAG-ASN         : angle       5.15731 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 59
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6347 (m-10)
REVERT: A  468 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8446 (m)
REVERT: A  562 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7054 (ttt180)
REVERT: A  679 MET cc_start: 0.1547 (mpp) cc_final: 0.1197 (tpt)
  outliers start: 45
  outliers final: 36
  residues processed: 99
  average time/residue: 0.0862
  time to fit residues: 13.2104
Evaluate side-chains
  95 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 56
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 121 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 131 optimal weight:   20.0000
   chunk 31 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 8 optimal weight:    0.1980
   chunk 15 optimal weight:    9.9990
   chunk 126 optimal weight:    4.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 HIS ** 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 = 0.4268 r_free = 0.4268 target = 0.185868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.164212 restraints weight = 17490.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.160932 restraints weight = 33602.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.159297 restraints weight = 31577.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.158914 restraints weight = 32754.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.157676 restraints weight = 25836.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10878  Z= 0.206
  Angle     :  0.684  15.877  14835  Z= 0.335
  Chirality :  0.047   0.631   1666
  Planarity :  0.005   0.082   1930
  Dihedral  :  5.740  54.765   1718
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.02 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 18.54 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.22), residues: 1346
  helix: -5.46 (0.23), residues: 6
  sheet:  0.76 (0.20), residues: 620
  loop : -1.07 (0.22), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 425 
 TYR   0.015   0.001   TYR A 109 
 PHE   0.029   0.002   PHE A 493 
 TRP   0.025   0.002   TRP A 273 
 HIS   0.002   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (10854)
  covalent geometry    : angle       0.65272 (14775)
  SS BOND              : bond        0.00262 (   12)
  SS BOND              : angle       0.76748 (   24)
  hydrogen bonds       : bond        0.03451 (  352)
  hydrogen bonds       : angle       5.18912 (  906)
  link_BETA1-4         : bond        0.00437 (    5)
  link_BETA1-4         : angle       2.28796 (   15)
  link_NAG-ASN         : bond        0.00771 (    7)
  link_NAG-ASN         : angle       5.14407 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 58
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.8012 (m-10)
REVERT: A  468 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8415 (m)
REVERT: A  562 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7044 (ttt180)
REVERT: B  233 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5595 (p0)
  outliers start: 49
  outliers final: 36
  residues processed: 102
  average time/residue: 0.0853
  time to fit residues: 13.4417
Evaluate side-chains
  95 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 55
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 130 optimal weight:    3.9990
   chunk 133 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 70 optimal weight:   20.0000
   chunk 58 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 99 optimal weight:    0.0770
   chunk 41 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.9942

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

Flipped N/Q/H residues before XYZ refinement:
A 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.188719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.167412 restraints weight = 17333.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.163037 restraints weight = 34397.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.162193 restraints weight = 34489.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.159783 restraints weight = 37057.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.158232 restraints weight = 37013.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10878  Z= 0.157
  Angle     :  0.662  15.540  14835  Z= 0.321
  Chirality :  0.046   0.613   1666
  Planarity :  0.005   0.077   1930
  Dihedral  :  5.506  52.886   1718
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.27 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.72 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.23), residues: 1346
  helix: -5.47 (0.23), residues: 6
  sheet:  0.80 (0.20), residues: 623
  loop : -1.00 (0.23), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 425 
 TYR   0.011   0.001   TYR A 109 
 PHE   0.030   0.002   PHE A 493 
 TRP   0.029   0.001   TRP A 273 
 HIS   0.002   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10854)
  covalent geometry    : angle       0.63161 (14775)
  SS BOND              : bond        0.00224 (   12)
  SS BOND              : angle       0.61232 (   24)
  hydrogen bonds       : bond        0.03061 (  352)
  hydrogen bonds       : angle       5.06274 (  906)
  link_BETA1-4         : bond        0.00403 (    5)
  link_BETA1-4         : angle       2.27416 (   15)
  link_NAG-ASN         : bond        0.00782 (    7)
  link_NAG-ASN         : angle       4.97667 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 58
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8403 (m)
REVERT: A  562 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7143 (ttt180)
REVERT: A  679 MET cc_start: 0.1607 (mpp) cc_final: 0.1071 (tpt)
REVERT: B  233 ASP cc_start: 0.6098 (OUTLIER) cc_final: 0.5622 (p0)
  outliers start: 46
  outliers final: 39
  residues processed: 97
  average time/residue: 0.0934
  time to fit residues: 13.5470
Evaluate side-chains
  96 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 54
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 33 optimal weight:    0.2980
   chunk 130 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 59 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 318 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 = 0.4286 r_free = 0.4286 target = 0.188806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.171915 restraints weight = 17380.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.166416 restraints weight = 25560.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.164265 restraints weight = 32514.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.163359 restraints weight = 35770.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.161969 restraints weight = 28933.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10878  Z= 0.154
  Angle     :  0.666  15.330  14835  Z= 0.324
  Chirality :  0.046   0.608   1666
  Planarity :  0.005   0.075   1930
  Dihedral  :  5.432  51.670   1718
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.50 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.99 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.23), residues: 1346
  helix: -5.45 (0.23), residues: 6
  sheet:  0.79 (0.21), residues: 611
  loop : -0.94 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  87 
 TYR   0.011   0.001   TYR B 405 
 PHE   0.030   0.002   PHE A 493 
 TRP   0.029   0.001   TRP A 273 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10854)
  covalent geometry    : angle       0.63634 (14775)
  SS BOND              : bond        0.00261 (   12)
  SS BOND              : angle       0.64270 (   24)
  hydrogen bonds       : bond        0.03008 (  352)
  hydrogen bonds       : angle       5.04362 (  906)
  link_BETA1-4         : bond        0.00423 (    5)
  link_BETA1-4         : angle       2.24317 (   15)
  link_NAG-ASN         : bond        0.00769 (    7)
  link_NAG-ASN         : angle       4.90404 (   21)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 54
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8426 (m)
REVERT: A  562 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7028 (ttt180)
REVERT: A  679 MET cc_start: 0.1466 (mpp) cc_final: 0.0879 (tpp)
REVERT: B  233 ASP cc_start: 0.6048 (OUTLIER) cc_final: 0.5612 (p0)
  outliers start: 44
  outliers final: 41
  residues processed: 92
  average time/residue: 0.0895
  time to fit residues: 12.7333
Evaluate side-chains
  96 residues out of total 1127 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 52
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  371 ASN
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  428 ILE
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  560 TYR
Chi-restraints excluded: chain A residue  562 ARG
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  575 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  673 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain B residue   79 GLU
Chi-restraints excluded: chain B residue  119 THR
Chi-restraints excluded: chain B residue  123 ARG
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  233 ASP
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ILE
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  348 CYS
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  424 VAL
Chi-restraints excluded: chain B residue  428 ILE
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 129 optimal weight:   10.0000
   chunk 122 optimal weight:    0.8980
   chunk 131 optimal weight:   20.0000
   chunk 108 optimal weight:    0.6980
   chunk 76 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9980
   chunk 133 optimal weight:    4.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4290 r_free = 0.4290 target = 0.189209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.172310 restraints weight = 17525.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.167482 restraints weight = 25365.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.164854 restraints weight = 28540.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.164189 restraints weight = 33829.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.163007 restraints weight = 27697.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10878  Z= 0.142
  Angle     :  0.651  15.017  14835  Z= 0.316
  Chirality :  0.045   0.596   1666
  Planarity :  0.004   0.074   1930
  Dihedral  :  5.265  49.583   1718
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.05 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.90 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.05 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.23), residues: 1346
  helix: -5.44 (0.23), residues: 6
  sheet:  0.80 (0.21), residues: 612
  loop : -0.86 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 314 
 TYR   0.011   0.001   TYR B 405 
 PHE   0.030   0.002   PHE A 493 
 TRP   0.029   0.001   TRP A 273 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10854)
  covalent geometry    : angle       0.62234 (14775)
  SS BOND              : bond        0.00208 (   12)
  SS BOND              : angle       0.52998 (   24)
  hydrogen bonds       : bond        0.02875 (  352)
  hydrogen bonds       : angle       4.95488 (  906)
  link_BETA1-4         : bond        0.00431 (    5)
  link_BETA1-4         : angle       2.21583 (   15)
  link_NAG-ASN         : bond        0.00769 (    7)
  link_NAG-ASN         : angle       4.78271 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1847.15 seconds
wall clock time: 32 minutes 37.39 seconds (1957.39 seconds total)