Starting phenix.real_space_refine
on Wed Jul 30 14:23:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2025/7fd8_31536.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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     114      5.16       5
     C    7824      2.51       5
     N    2004      2.21       5
     O    2210      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12152
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 764, 6014
          Classifications: {'peptide': 764}
          Link IDs: {'PTRANS': 32, 'TRANS': 731}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 62
          Unusual residues: {'NAG': 1, 'QUS': 1, 'Y01': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 13.99, per 1000 atoms: 1.15
  Number of scatterers: 12152
  At special positions: 0
  Unit cell: (77.43, 102.35, 173.55, 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     114     16.00
     O    2210      8.00
     N    2004      7.00
     C    7824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 530 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 278 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 537 " - pdb=" SG  CYS A 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 552 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 644 " - pdb=" SG  CYS A 733 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 530 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 278 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 419 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 552 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 733 " distance=2.04

  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
    NAG-ASN
      " NAG A 901 " - " ASN A 210 "
      " NAG B 901 " - " ASN B 210 "
  Time building additional restraints: 2.98
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2852

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 12 sheets defined
      48.4% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 81
    Processing helix  chain 'A' and resid 101 through 113
    Processing helix  chain 'A' and resid 151 through 163
      removed outlier: 3.800A  pdb=" N   LEU A 161 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.776A  pdb=" N   ASP A 181 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 209
    Processing helix  chain 'A' and resid 221 through 238
    Processing helix  chain 'A' and resid 253 through 266
    Processing helix  chain 'A' and resid 279 through 293
    Processing helix  chain 'A' and resid 317 through 321
      removed outlier: 3.521A  pdb=" N   ALA A 321 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
    Processing helix  chain 'A' and resid 354 through 364
      removed outlier: 3.815A  pdb=" N   PHE A 363 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 419
    Processing helix  chain 'A' and resid 433 through 444
      removed outlier: 3.669A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 604
      removed outlier: 3.517A  pdb=" N   ALA A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 614 through 636
      removed outlier: 3.862A  pdb=" N   THR A 632 " --> pdb=" O   GLY A 628 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 671
      removed outlier: 3.737A  pdb=" N   ARG A 648 " --> pdb=" O   CYS A 644 " (cutoff:3.500A)
      Proline residue:  A 655  - end of helix
    Processing helix  chain 'A' and resid 692 through 715
      removed outlier: 3.943A  pdb=" N   GLN A 704 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 760
      Proline residue:  A 743  - end of helix
    Processing helix  chain 'A' and resid 765 through 788
      removed outlier: 5.756A  pdb=" N   ALA A 771 " --> pdb=" O   ASN A 767 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 795
      removed outlier: 4.274A  pdb=" N   PHE A 793 " --> pdb=" O   VAL A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 816
    Processing helix  chain 'A' and resid 818 through 826
    Processing helix  chain 'B' and resid 65 through 81
    Processing helix  chain 'B' and resid 101 through 113
    Processing helix  chain 'B' and resid 151 through 163
      removed outlier: 3.798A  pdb=" N   LEU B 161 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 181
      removed outlier: 3.776A  pdb=" N   ASP B 181 " --> pdb=" O   ASP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 209
    Processing helix  chain 'B' and resid 221 through 238
    Processing helix  chain 'B' and resid 253 through 266
    Processing helix  chain 'B' and resid 279 through 293
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.522A  pdb=" N   ALA B 321 " --> pdb=" O   GLN B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 342
    Processing helix  chain 'B' and resid 354 through 364
      removed outlier: 3.814A  pdb=" N   PHE B 363 " --> pdb=" O   TRP B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 419
    Processing helix  chain 'B' and resid 433 through 444
      removed outlier: 3.669A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 604
      removed outlier: 3.517A  pdb=" N   ALA B 583 " --> pdb=" O   GLU B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 614 through 636
      removed outlier: 3.862A  pdb=" N   THR B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE B 633 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 671
      removed outlier: 3.737A  pdb=" N   ARG B 648 " --> pdb=" O   CYS B 644 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
    Processing helix  chain 'B' and resid 692 through 715
      removed outlier: 3.943A  pdb=" N   GLN B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 760
      Proline residue:  B 743  - end of helix
    Processing helix  chain 'B' and resid 765 through 788
      removed outlier: 5.757A  pdb=" N   ALA B 771 " --> pdb=" O   ASN B 767 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   LYS B 772 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 795
      removed outlier: 4.275A  pdb=" N   PHE B 793 " --> pdb=" O   VAL B 789 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 816
    Processing helix  chain 'B' and resid 818 through 826
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
      removed outlier: 5.827A  pdb=" N   ILE A  35 " --> pdb=" O   GLY A  92 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   GLU A  94 " --> pdb=" O   ILE A  35 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ILE A  37 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   ARG A  96 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ALA A  39 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ILE A  36 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   GLY A  38 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 8.610A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 219
      removed outlier: 7.713A  pdb=" N   VAL A 214 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   SER A 245 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   ALA A 216 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   LYS A 247 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276
      removed outlier: 6.241A  pdb=" N   VAL A 274 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 325 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 327 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY A 324 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR A 466 " --> pdb=" O   SER A 486 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   SER A 486 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE A 468 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447
      removed outlier: 3.523A  pdb=" N   PHE A 446 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523
      removed outlier: 3.571A  pdb=" N   THR A 535 " --> pdb=" O   LYS A 521 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722
    Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31
      removed outlier: 5.827A  pdb=" N   ILE B  35 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   GLU B  94 " --> pdb=" O   ILE B  35 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ILE B  37 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   ARG B  96 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ALA B  39 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ILE B  36 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   GLY B  38 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 8.611A  pdb=" N   ILE B 170 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 219
      removed outlier: 7.712A  pdb=" N   VAL B 214 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER B 245 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ALA B 216 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LYS B 247 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   HIS B 218 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 276
      removed outlier: 6.240A  pdb=" N   VAL B 274 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE B 325 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 327 " --> pdb=" O   GLY B 303 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLY B 324 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR B 466 " --> pdb=" O   SER B 486 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   SER B 486 " --> pdb=" O   TYR B 466 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B 468 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 447
      removed outlier: 3.523A  pdb=" N   PHE B 446 " --> pdb=" O   ILE B 454 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 520 through 523
      removed outlier: 3.570A  pdb=" N   THR B 535 " --> pdb=" O   LYS B 521 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722

    576 hydrogen bonds defined for protein.
    1692 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: 3.88

  Time building geometry restraints manager: 3.58 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1946
        1.30 -     1.43: 3302
        1.43 -     1.56: 7022
        1.56 -     1.69: 0
        1.69 -     1.82: 164
  Bond restraints: 12434
  Sorted by residual:
  bond pdb=" CAY Y01 B 903 "
       pdb=" OAG Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.207  1.422 -0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" CAY Y01 A 903 "
       pdb=" OAG Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.207  1.422 -0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" CAI Y01 B 903 "
       pdb=" CAZ Y01 B 903 "
    ideal  model  delta    sigma   weight residual
    1.332  1.498 -0.166 2.00e-02 2.50e+03 6.93e+01
  bond pdb=" CAI Y01 A 903 "
       pdb=" CAZ Y01 A 903 "
    ideal  model  delta    sigma   weight residual
    1.332  1.498 -0.166 2.00e-02 2.50e+03 6.93e+01
  bond pdb=" C01 QUS A 902 "
       pdb=" C02 QUS A 902 "
    ideal  model  delta    sigma   weight residual
    1.556  1.458  0.098 2.00e-02 2.50e+03 2.41e+01
  ... (remaining 12429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 14746
        2.01 -     4.03: 1950
        4.03 -     6.04: 134
        6.04 -     8.05: 22
        8.05 -    10.06: 10
  Bond angle restraints: 16862
  Sorted by residual:
  angle pdb=" C   LYS B 379 "
        pdb=" N   THR B 380 "
        pdb=" CA  THR B 380 "
      ideal   model   delta    sigma   weight residual
     121.31  127.44   -6.13 1.49e+00 4.50e-01 1.69e+01
  angle pdb=" C   LYS A 379 "
        pdb=" N   THR A 380 "
        pdb=" CA  THR A 380 "
      ideal   model   delta    sigma   weight residual
     121.31  127.36   -6.05 1.49e+00 4.50e-01 1.65e+01
  angle pdb=" N   LYS B 517 "
        pdb=" CA  LYS B 517 "
        pdb=" C   LYS B 517 "
      ideal   model   delta    sigma   weight residual
     112.57  108.07    4.50 1.13e+00 7.83e-01 1.58e+01
  angle pdb=" N   LYS A 517 "
        pdb=" CA  LYS A 517 "
        pdb=" C   LYS A 517 "
      ideal   model   delta    sigma   weight residual
     112.57  108.09    4.48 1.13e+00 7.83e-01 1.57e+01
  angle pdb=" C   TYR A 317 "
        pdb=" N   GLN A 318 "
        pdb=" CA  GLN A 318 "
      ideal   model   delta    sigma   weight residual
     120.28  125.90   -5.62 1.44e+00 4.82e-01 1.52e+01
  ... (remaining 16857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.63: 7278
       22.63 -    45.25: 247
       45.25 -    67.88: 45
       67.88 -    90.50: 18
       90.50 -   113.13: 14
  Dihedral angle restraints: 7602
    sinusoidal: 3154
      harmonic: 4448
  Sorted by residual:
  dihedral pdb=" CB  CYS B 537 "
           pdb=" SG  CYS B 537 "
           pdb=" SG  CYS B 549 "
           pdb=" CB  CYS B 549 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.64  -63.64     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS A 537 "
           pdb=" SG  CYS A 537 "
           pdb=" SG  CYS A 549 "
           pdb=" CB  CYS A 549 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.63  -63.63     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS A 552 "
           pdb=" SG  CYS A 552 "
           pdb=" SG  CYS A 565 "
           pdb=" CB  CYS A 565 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -129.41   43.41     1      1.00e+01 1.00e-02 2.63e+01
  ... (remaining 7599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.345: 1892
       0.345 -    0.689: 4
       0.689 -    1.033: 0
       1.033 -    1.378: 0
       1.378 -    1.722: 2
  Chirality restraints: 1898
  Sorted by residual:
  chirality pdb=" C02 QUS B 902 "
            pdb=" C01 QUS B 902 "
            pdb=" C03 QUS B 902 "
            pdb=" NP3 QUS B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    0.78    1.72 2.00e-01 2.50e+01 7.41e+01
  chirality pdb=" C02 QUS A 902 "
            pdb=" C01 QUS A 902 "
            pdb=" C03 QUS A 902 "
            pdb=" NP3 QUS A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    0.78    1.72 2.00e-01 2.50e+01 7.38e+01
  chirality pdb=" C1  NAG B 901 "
            pdb=" ND2 ASN B 210 "
            pdb=" C2  NAG B 901 "
            pdb=" O5  NAG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.88   -0.52 2.00e-01 2.50e+01 6.75e+00
  ... (remaining 1895 not shown)

  Planarity restraints: 2116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 B 903 "   -0.025 2.00e-02 2.50e+03   4.43e-02 1.97e+01
        pdb=" CAY Y01 B 903 "    0.077 2.00e-02 2.50e+03
        pdb=" OAG Y01 B 903 "   -0.027 2.00e-02 2.50e+03
        pdb=" OAW Y01 B 903 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAM Y01 A 903 "    0.025 2.00e-02 2.50e+03   4.35e-02 1.89e+01
        pdb=" CAY Y01 A 903 "   -0.075 2.00e-02 2.50e+03
        pdb=" OAG Y01 A 903 "    0.027 2.00e-02 2.50e+03
        pdb=" OAW Y01 A 903 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C01 QUS B 902 "   -0.046 2.00e-02 2.50e+03   2.64e-02 6.99e+00
        pdb=" C02 QUS B 902 "    0.013 2.00e-02 2.50e+03
        pdb=" O16 QUS B 902 "    0.016 2.00e-02 2.50e+03
        pdb=" O17 QUS B 902 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2113 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3556
        2.84 -     3.36: 11937
        3.36 -     3.87: 20567
        3.87 -     4.39: 23303
        4.39 -     4.90: 39011
  Nonbonded interactions: 98374
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 250 "
            pdb=" OE2 GLU B 279 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OG  SER A 250 "
            pdb=" OE2 GLU A 279 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   GLY B 253 "
            pdb=" OG  SER B 256 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   GLY A 253 "
            pdb=" OG  SER A 256 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OG  SER A 152 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.339 3.040
  ... (remaining 98369 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             5.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     37.120
  Find NCS groups from input model:        0.420
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
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      :  0.008   0.215  12456  Z= 0.494
  Angle     :  1.403  10.063  16908  Z= 0.935
  Chirality :  0.108   1.722   1898
  Planarity :  0.004   0.044   2114
  Dihedral  : 13.892 113.126   4690
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.58 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  2.88 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.25 (0.19), residues: 1516
  helix: -0.64 (0.16), residues: 706
  sheet: -2.08 (0.37), residues: 160
  loop : -2.24 (0.23), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP A 575 
 HIS   0.010   0.002   HIS B  74 
 PHE   0.020   0.002   PHE B 337 
 TYR   0.019   0.002   TYR B 223 
 ARG   0.005   0.001   ARG A 351 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00930 (    2)
  link_NAG-ASN         : angle       5.28140 (    6)
  hydrogen bonds       : bond        0.12851 (  576)
  hydrogen bonds       : angle       5.79304 ( 1692)
  SS BOND              : bond        0.00335 (   20)
  SS BOND              : angle       1.52857 (   40)
  covalent geometry    : bond        0.00800 (12434)
  covalent geometry    : angle       1.39914 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.8661 (ttt) cc_final: 0.8382 (tmm)
REVERT: A  429 MET cc_start: 0.7534 (mpp) cc_final: 0.7218 (mpp)
REVERT: A  592 LEU cc_start: 0.8961 (mt) cc_final: 0.8749 (tt)
REVERT: A  714 MET cc_start: 0.6864 (mmt) cc_final: 0.5929 (ttp)
REVERT: B  414 MET cc_start: 0.8632 (ttt) cc_final: 0.8427 (tmm)
REVERT: B  429 MET cc_start: 0.7558 (mpp) cc_final: 0.7267 (mpp)
REVERT: B  592 LEU cc_start: 0.8903 (mt) cc_final: 0.8699 (tt)
REVERT: B  714 MET cc_start: 0.7060 (mmt) cc_final: 0.6244 (ttp)
  outliers start: 8
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2598
  time to fit residues: 50.4686
Evaluate side-chains
  72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 138 optimal weight:   20.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
A 390 HIS
B 159 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.064518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.048000 restraints weight = 63855.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.047898 restraints weight = 38220.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048179 restraints weight = 29982.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12456  Z= 0.203
  Angle     :  0.665  10.949  16908  Z= 0.328
  Chirality :  0.043   0.198   1898
  Planarity :  0.003   0.038   2114
  Dihedral  :  9.510  74.761   1862
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.15 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  6.74 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.21), residues: 1516
  helix:  0.51 (0.19), residues: 732
  sheet: -2.26 (0.32), residues: 178
  loop : -1.83 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 532 
 HIS   0.006   0.001   HIS B  74 
 PHE   0.016   0.001   PHE B 337 
 TYR   0.011   0.001   TYR A 317 
 ARG   0.004   0.001   ARG B 574 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00140 (    2)
  link_NAG-ASN         : angle       2.72729 (    6)
  hydrogen bonds       : bond        0.04074 (  576)
  hydrogen bonds       : angle       4.62338 ( 1692)
  SS BOND              : bond        0.00305 (   20)
  SS BOND              : angle       0.87982 (   40)
  covalent geometry    : bond        0.00438 (12434)
  covalent geometry    : angle       0.66223 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9094 (ttt) cc_final: 0.8589 (tmm)
REVERT: A  714 MET cc_start: 0.6975 (mmt) cc_final: 0.6165 (ttp)
REVERT: B  414 MET cc_start: 0.9083 (ttt) cc_final: 0.8623 (tmm)
REVERT: B  714 MET cc_start: 0.7175 (mmt) cc_final: 0.6337 (ttp)
  outliers start: 8
  outliers final: 5
  residues processed: 87
  average time/residue: 0.2131
  time to fit residues: 29.2090
Evaluate side-chains
  72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 135 optimal weight:    3.9990
   chunk 149 optimal weight:    0.0670
   chunk 22 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 114 optimal weight:    0.0270
   chunk 122 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 704 GLN
** B  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.065183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.049227 restraints weight = 65108.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.048399 restraints weight = 38818.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.049250 restraints weight = 30999.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12456  Z= 0.138
  Angle     :  0.590   9.683  16908  Z= 0.291
  Chirality :  0.042   0.227   1898
  Planarity :  0.003   0.036   2114
  Dihedral  :  7.947  59.703   1862
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.28 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  7.88 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.22), residues: 1516
  helix:  1.13 (0.19), residues: 720
  sheet: -2.00 (0.34), residues: 170
  loop : -1.68 (0.26), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 532 
 HIS   0.004   0.001   HIS A  74 
 PHE   0.010   0.001   PHE A 596 
 TYR   0.008   0.001   TYR A 341 
 ARG   0.004   0.000   ARG B 574 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00574 (    2)
  link_NAG-ASN         : angle       2.64830 (    6)
  hydrogen bonds       : bond        0.03622 (  576)
  hydrogen bonds       : angle       4.34320 ( 1692)
  SS BOND              : bond        0.00197 (   20)
  SS BOND              : angle       0.84839 (   40)
  covalent geometry    : bond        0.00299 (12434)
  covalent geometry    : angle       0.58694 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 1.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9042 (ttt) cc_final: 0.8688 (tmm)
REVERT: A  429 MET cc_start: 0.8044 (mpp) cc_final: 0.7646 (mpp)
REVERT: A  714 MET cc_start: 0.7008 (mmt) cc_final: 0.6162 (ttp)
REVERT: B  414 MET cc_start: 0.9024 (ttt) cc_final: 0.8674 (tmm)
REVERT: B  429 MET cc_start: 0.8078 (mpp) cc_final: 0.7721 (mpp)
REVERT: B  657 MET cc_start: 0.9489 (ptm) cc_final: 0.9017 (ppp)
REVERT: B  714 MET cc_start: 0.7201 (mmt) cc_final: 0.6385 (ttp)
  outliers start: 15
  outliers final: 9
  residues processed: 84
  average time/residue: 0.3569
  time to fit residues: 45.6774
Evaluate side-chains
  75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 1.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 50 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 19 optimal weight:    0.5980
   chunk 113 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   overall best weight:    3.3188

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

Flipped N/Q/H residues before XYZ refinement:
** B 704 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 = 0.3503 r_free = 0.3503 target = 0.063654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.046915 restraints weight = 64878.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.047298 restraints weight = 38024.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.047628 restraints weight = 29366.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12456  Z= 0.262
  Angle     :  0.652   8.561  16908  Z= 0.328
  Chirality :  0.043   0.156   1898
  Planarity :  0.004   0.041   2114
  Dihedral  :  7.631  69.539   1862
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.00 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.64 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.22), residues: 1516
  helix:  1.18 (0.19), residues: 720
  sheet: -2.19 (0.34), residues: 180
  loop : -1.57 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 532 
 HIS   0.006   0.001   HIS B  74 
 PHE   0.016   0.002   PHE A 596 
 TYR   0.010   0.001   TYR B 340 
 ARG   0.004   0.001   ARG B 351 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00061 (    2)
  link_NAG-ASN         : angle       2.04647 (    6)
  hydrogen bonds       : bond        0.03814 (  576)
  hydrogen bonds       : angle       4.63265 ( 1692)
  SS BOND              : bond        0.00351 (   20)
  SS BOND              : angle       0.82521 (   40)
  covalent geometry    : bond        0.00564 (12434)
  covalent geometry    : angle       0.65088 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 2.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  407 MET cc_start: 0.9260 (tpp) cc_final: 0.8988 (tpp)
REVERT: A  414 MET cc_start: 0.9128 (ttt) cc_final: 0.8792 (tmm)
REVERT: A  429 MET cc_start: 0.8022 (mpp) cc_final: 0.7694 (mpp)
REVERT: A  494 MET cc_start: 0.7893 (ptp) cc_final: 0.7669 (ptp)
REVERT: A  714 MET cc_start: 0.7144 (mmt) cc_final: 0.6224 (ttp)
REVERT: B  407 MET cc_start: 0.9258 (tpp) cc_final: 0.8984 (tpp)
REVERT: B  414 MET cc_start: 0.9122 (ttt) cc_final: 0.8768 (tmm)
REVERT: B  429 MET cc_start: 0.8025 (mpp) cc_final: 0.7743 (mpp)
REVERT: B  657 MET cc_start: 0.9395 (ptm) cc_final: 0.8966 (ppp)
REVERT: B  714 MET cc_start: 0.7325 (mmt) cc_final: 0.6331 (ttp)
  outliers start: 23
  outliers final: 19
  residues processed: 90
  average time/residue: 0.3363
  time to fit residues: 47.6945
Evaluate side-chains
  86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 139 optimal weight:    9.9990
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 125 optimal weight:    9.9990
   chunk 129 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 135 optimal weight:    4.9990
   chunk 126 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B 704 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 = 0.3483 r_free = 0.3483 target = 0.063306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.046768 restraints weight = 63172.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.046506 restraints weight = 37078.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.047100 restraints weight = 27921.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  12456  Z= 0.274
  Angle     :  0.656   8.690  16908  Z= 0.331
  Chirality :  0.044   0.157   1898
  Planarity :  0.004   0.040   2114
  Dihedral  :  7.210  69.176   1862
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.33 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.39 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.22), residues: 1516
  helix:  1.15 (0.19), residues: 718
  sheet: -2.11 (0.35), residues: 176
  loop : -1.58 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 532 
 HIS   0.005   0.001   HIS A  74 
 PHE   0.017   0.002   PHE A 596 
 TYR   0.010   0.001   TYR B 340 
 ARG   0.003   0.001   ARG B 310 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00076 (    2)
  link_NAG-ASN         : angle       2.19681 (    6)
  hydrogen bonds       : bond        0.03857 (  576)
  hydrogen bonds       : angle       4.71277 ( 1692)
  SS BOND              : bond        0.00352 (   20)
  SS BOND              : angle       0.81124 (   40)
  covalent geometry    : bond        0.00587 (12434)
  covalent geometry    : angle       0.65443 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 70
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9099 (ttt) cc_final: 0.8761 (tmm)
REVERT: A  429 MET cc_start: 0.7956 (mpp) cc_final: 0.7722 (mpp)
REVERT: A  494 MET cc_start: 0.7891 (ptp) cc_final: 0.7684 (ptp)
REVERT: A  657 MET cc_start: 0.9469 (ptm) cc_final: 0.9019 (ppp)
REVERT: A  714 MET cc_start: 0.7099 (mmt) cc_final: 0.6302 (ttp)
REVERT: B  414 MET cc_start: 0.9096 (ttt) cc_final: 0.8764 (tmm)
REVERT: B  429 MET cc_start: 0.8022 (mpp) cc_final: 0.7765 (mpp)
REVERT: B  657 MET cc_start: 0.9435 (ptm) cc_final: 0.9147 (tmm)
REVERT: B  714 MET cc_start: 0.7228 (mmt) cc_final: 0.6328 (ttp)
REVERT: B  778 MET cc_start: 0.9115 (mmm) cc_final: 0.8311 (tpt)
  outliers start: 31
  outliers final: 22
  residues processed: 100
  average time/residue: 0.2165
  time to fit residues: 32.8969
Evaluate side-chains
  89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  575 TRP
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  575 TRP
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  699 ILE
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 137 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 108 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 139 optimal weight:   20.0000
   chunk 132 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 704 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.065275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.048627 restraints weight = 63625.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.048826 restraints weight = 36706.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049399 restraints weight = 25997.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12456  Z= 0.117
  Angle     :  0.564  10.114  16908  Z= 0.277
  Chirality :  0.041   0.179   1898
  Planarity :  0.003   0.042   2114
  Dihedral  :  6.539  61.553   1862
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.34 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.38 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.22), residues: 1516
  helix:  1.53 (0.19), residues: 722
  sheet: -1.67 (0.36), residues: 170
  loop : -1.54 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 354 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.010   0.001   PHE B 337 
 TYR   0.007   0.001   TYR B 340 
 ARG   0.003   0.000   ARG B 574 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00421 (    2)
  link_NAG-ASN         : angle       1.71854 (    6)
  hydrogen bonds       : bond        0.03342 (  576)
  hydrogen bonds       : angle       4.28397 ( 1692)
  SS BOND              : bond        0.00163 (   20)
  SS BOND              : angle       0.82261 (   40)
  covalent geometry    : bond        0.00253 (12434)
  covalent geometry    : angle       0.56246 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9115 (ttt) cc_final: 0.8737 (tmm)
REVERT: A  714 MET cc_start: 0.7147 (mmt) cc_final: 0.6284 (ttp)
REVERT: B  414 MET cc_start: 0.9104 (ttt) cc_final: 0.8730 (tmm)
REVERT: B  657 MET cc_start: 0.9398 (ptm) cc_final: 0.9068 (ppp)
REVERT: B  714 MET cc_start: 0.7221 (mmt) cc_final: 0.6456 (ttp)
  outliers start: 16
  outliers final: 13
  residues processed: 86
  average time/residue: 0.2280
  time to fit residues: 30.1832
Evaluate side-chains
  81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  630 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 147 optimal weight:    7.9990
   chunk 117 optimal weight:    6.9990
   chunk 133 optimal weight:    4.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.064357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.047763 restraints weight = 63955.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.047708 restraints weight = 37013.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.048273 restraints weight = 26763.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12456  Z= 0.189
  Angle     :  0.599   9.104  16908  Z= 0.298
  Chirality :  0.042   0.157   1898
  Planarity :  0.003   0.040   2114
  Dihedral  :  6.547  66.631   1862
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.47 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.83 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.22), residues: 1516
  helix:  1.50 (0.19), residues: 720
  sheet: -1.44 (0.37), residues: 166
  loop : -1.41 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 532 
 HIS   0.004   0.001   HIS B  74 
 PHE   0.013   0.001   PHE A 337 
 TYR   0.009   0.001   TYR A 340 
 ARG   0.002   0.000   ARG A 574 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00192 (    2)
  link_NAG-ASN         : angle       1.65364 (    6)
  hydrogen bonds       : bond        0.03513 (  576)
  hydrogen bonds       : angle       4.43759 ( 1692)
  SS BOND              : bond        0.00227 (   20)
  SS BOND              : angle       0.77140 (   40)
  covalent geometry    : bond        0.00409 (12434)
  covalent geometry    : angle       0.59746 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8320 (mmt) cc_final: 0.8011 (mmp)
REVERT: A  414 MET cc_start: 0.9116 (ttt) cc_final: 0.8747 (tmm)
REVERT: A  657 MET cc_start: 0.9017 (tmm) cc_final: 0.8675 (ppp)
REVERT: A  714 MET cc_start: 0.7136 (mmt) cc_final: 0.6276 (ttp)
REVERT: B  414 MET cc_start: 0.9120 (ttt) cc_final: 0.8746 (tmm)
REVERT: B  714 MET cc_start: 0.7186 (mmt) cc_final: 0.6597 (mtp)
  outliers start: 23
  outliers final: 19
  residues processed: 89
  average time/residue: 0.2040
  time to fit residues: 28.5952
Evaluate side-chains
  86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 139 optimal weight:   20.0000
   chunk 103 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 146 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.065379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049216 restraints weight = 64236.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.048871 restraints weight = 36639.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.049056 restraints weight = 28945.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12456  Z= 0.119
  Angle     :  0.573   9.591  16908  Z= 0.281
  Chirality :  0.041   0.169   1898
  Planarity :  0.003   0.040   2114
  Dihedral  :  6.225  61.947   1862
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.29 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.22), residues: 1516
  helix:  1.59 (0.19), residues: 720
  sheet: -1.34 (0.38), residues: 166
  loop : -1.34 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 532 
 HIS   0.002   0.001   HIS B  74 
 PHE   0.010   0.001   PHE A 337 
 TYR   0.007   0.001   TYR B 723 
 ARG   0.003   0.000   ARG A 574 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00397 (    2)
  link_NAG-ASN         : angle       1.55854 (    6)
  hydrogen bonds       : bond        0.03315 (  576)
  hydrogen bonds       : angle       4.26506 ( 1692)
  SS BOND              : bond        0.00158 (   20)
  SS BOND              : angle       0.80923 (   40)
  covalent geometry    : bond        0.00258 (12434)
  covalent geometry    : angle       0.57162 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 1.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9137 (ttt) cc_final: 0.8739 (tmm)
REVERT: A  601 PHE cc_start: 0.7173 (m-80) cc_final: 0.6969 (m-80)
REVERT: A  657 MET cc_start: 0.9030 (tmm) cc_final: 0.8681 (ppp)
REVERT: A  714 MET cc_start: 0.7203 (mmt) cc_final: 0.6531 (ttp)
REVERT: B  414 MET cc_start: 0.9134 (ttt) cc_final: 0.8736 (tmm)
REVERT: B  657 MET cc_start: 0.9301 (ptt) cc_final: 0.8926 (ppp)
REVERT: B  714 MET cc_start: 0.7260 (mmt) cc_final: 0.6683 (mtp)
  outliers start: 21
  outliers final: 17
  residues processed: 88
  average time/residue: 0.2132
  time to fit residues: 29.4785
Evaluate side-chains
  85 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  405 TYR
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 119 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0970
   chunk 77 optimal weight:    0.9990
   chunk 113 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.065742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.049808 restraints weight = 63929.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.049472 restraints weight = 34517.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.050042 restraints weight = 28220.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12456  Z= 0.104
  Angle     :  0.571   9.373  16908  Z= 0.277
  Chirality :  0.041   0.170   1898
  Planarity :  0.003   0.040   2114
  Dihedral  :  6.005  60.519   1862
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.62 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.14 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.22), residues: 1516
  helix:  1.80 (0.19), residues: 714
  sheet: -1.29 (0.39), residues: 172
  loop : -1.22 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 487 
 HIS   0.002   0.001   HIS A  44 
 PHE   0.009   0.001   PHE B 337 
 TYR   0.008   0.001   TYR A 340 
 ARG   0.007   0.000   ARG A 292 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00429 (    2)
  link_NAG-ASN         : angle       1.39844 (    6)
  hydrogen bonds       : bond        0.03177 (  576)
  hydrogen bonds       : angle       4.09192 ( 1692)
  SS BOND              : bond        0.00131 (   20)
  SS BOND              : angle       0.84925 (   40)
  covalent geometry    : bond        0.00224 (12434)
  covalent geometry    : angle       0.56958 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 MET cc_start: 0.9139 (ttt) cc_final: 0.8704 (tmm)
REVERT: A  601 PHE cc_start: 0.7353 (m-80) cc_final: 0.7136 (m-80)
REVERT: A  657 MET cc_start: 0.9074 (tmm) cc_final: 0.8740 (ppp)
REVERT: A  714 MET cc_start: 0.7038 (mmt) cc_final: 0.6402 (ttm)
REVERT: B  414 MET cc_start: 0.9110 (ttt) cc_final: 0.8764 (tmm)
REVERT: B  657 MET cc_start: 0.9319 (ptt) cc_final: 0.8925 (ppp)
REVERT: B  714 MET cc_start: 0.7152 (mmt) cc_final: 0.6547 (ttp)
  outliers start: 19
  outliers final: 15
  residues processed: 87
  average time/residue: 0.2119
  time to fit residues: 28.8690
Evaluate side-chains
  83 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 44 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 105 optimal weight:    0.3980
   chunk 59 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0470
   chunk 149 optimal weight:    0.0870
   chunk 146 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    0.3456

-------------------------------------------------------------------------------
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 = 0.3575 r_free = 0.3575 target = 0.066356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.049890 restraints weight = 63992.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.050503 restraints weight = 35322.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.050903 restraints weight = 23245.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12456  Z= 0.095
  Angle     :  0.557   8.869  16908  Z= 0.270
  Chirality :  0.041   0.170   1898
  Planarity :  0.003   0.044   2114
  Dihedral  :  5.715  58.880   1862
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.02 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.59 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.23), residues: 1516
  helix:  1.89 (0.19), residues: 718
  sheet: -1.48 (0.38), residues: 184
  loop : -1.00 (0.27), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 487 
 HIS   0.002   0.000   HIS A  44 
 PHE   0.008   0.001   PHE B 337 
 TYR   0.007   0.001   TYR A 340 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00421 (    2)
  link_NAG-ASN         : angle       1.34951 (    6)
  hydrogen bonds       : bond        0.03036 (  576)
  hydrogen bonds       : angle       3.98547 ( 1692)
  SS BOND              : bond        0.00181 (   20)
  SS BOND              : angle       0.87039 (   40)
  covalent geometry    : bond        0.00202 (12434)
  covalent geometry    : angle       0.55552 (16862)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 1.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 ASP cc_start: 0.8560 (p0) cc_final: 0.8348 (p0)
REVERT: A  414 MET cc_start: 0.9124 (ttt) cc_final: 0.8691 (tmm)
REVERT: A  573 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6434 (pp)
REVERT: A  657 MET cc_start: 0.9058 (tmm) cc_final: 0.8716 (ppp)
REVERT: A  714 MET cc_start: 0.7020 (mmt) cc_final: 0.6281 (ttm)
REVERT: B  305 ASP cc_start: 0.8542 (p0) cc_final: 0.8317 (p0)
REVERT: B  414 MET cc_start: 0.9122 (ttt) cc_final: 0.8672 (tmm)
REVERT: B  573 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6230 (pp)
REVERT: B  657 MET cc_start: 0.9267 (ptt) cc_final: 0.8899 (ppp)
REVERT: B  714 MET cc_start: 0.7107 (mmt) cc_final: 0.6554 (ttm)
  outliers start: 14
  outliers final: 11
  residues processed: 91
  average time/residue: 0.2242
  time to fit residues: 32.2877
Evaluate side-chains
  84 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 PHE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  573 LEU
Chi-restraints excluded: chain A residue  819 VAL
Chi-restraints excluded: chain B residue  112 PHE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  405 TYR
Chi-restraints excluded: chain B residue  573 LEU
Chi-restraints excluded: chain B residue  819 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 123 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 69 optimal weight:    9.9990
   chunk 118 optimal weight:    0.8980
   chunk 7 optimal weight:    7.9990
   chunk 121 optimal weight:    7.9990
   chunk 108 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 102 optimal weight:    3.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 157 GLN
B 157 GLN
B 693 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.066009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.049546 restraints weight = 63810.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.050148 restraints weight = 35680.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.050586 restraints weight = 23238.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12456  Z= 0.107
  Angle     :  0.586   9.983  16908  Z= 0.282
  Chirality :  0.041   0.211   1898
  Planarity :  0.003   0.044   2114
  Dihedral  :  5.733  61.416   1862
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.35 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.36 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1516
  helix:  1.87 (0.19), residues: 718
  sheet: -1.42 (0.39), residues: 184
  loop : -0.93 (0.28), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.002   0.001   HIS A  74 
 PHE   0.009   0.001   PHE B 337 
 TYR   0.008   0.001   TYR B 779 
 ARG   0.003   0.000   ARG B 351 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00366 (    2)
  link_NAG-ASN         : angle       1.31001 (    6)
  hydrogen bonds       : bond        0.03112 (  576)
  hydrogen bonds       : angle       4.04800 ( 1692)
  SS BOND              : bond        0.00143 (   20)
  SS BOND              : angle       0.82488 (   40)
  covalent geometry    : bond        0.00234 (12434)
  covalent geometry    : angle       0.58523 (16862)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3387.06 seconds
wall clock time: 61 minutes 25.12 seconds (3685.12 seconds total)