Starting phenix.real_space_refine
on Wed Sep 17 14:59:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ba5_44396/09_2025/9ba5_44396.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic.
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      42      5.16       5
     C    5666      2.51       5
     N    1570      2.21       5
     O    1734      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9012
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4436
          Classifications: {'peptide': 573}
          Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535}
    Chain: "B"
      Number of atoms: 4436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 573, 4436
          Classifications: {'peptide': 573}
          Link IDs: {'PCIS': 6, 'PTRANS': 31, 'TRANS': 535}
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.11, per 1000 atoms: 0.23
  Number of scatterers: 9012
  At special positions: 0
  Unit cell: (197.4, 80.85, 99.75, 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      42     16.00
     O    1734      8.00
     N    1570      7.00
     C    5666      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  61 " - pdb=" SG  CYS A 111 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 261 " - pdb=" SG  CYS A 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 348 " - pdb=" SG  CYS A 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 440 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 587 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  61 " - pdb=" SG  CYS B 111 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 261 " - pdb=" SG  CYS B 306 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 348 " - pdb=" SG  CYS B 395 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 440 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 530 " - pdb=" SG  CYS B 587 " distance=2.02

  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 701 " - " ASN A  76 "
      " NAG A 702 " - " ASN A 198 "
      " NAG A 703 " - " ASN A 461 "
      " NAG A 704 " - " ASN A 498 "
      " NAG A 705 " - " ASN A 525 "
      " NAG B 701 " - " ASN B  76 "
      " NAG B 702 " - " ASN B 198 "
      " NAG B 703 " - " ASN B 461 "
      " NAG B 704 " - " ASN B 498 "
      " NAG B 705 " - " ASN B 525 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 291.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 38 sheets defined
      4.5% alpha, 43.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 106
      removed outlier: 4.236A  pdb=" N   ALA A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 202
      removed outlier: 4.226A  pdb=" N   LEU A 202 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.774A  pdb=" N   SER A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.936A  pdb=" N   GLU A 483 " --> pdb=" O   ARG A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 4.124A  pdb=" N   GLY A 582 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 106
      removed outlier: 4.002A  pdb=" N   ALA B 106 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 202
      removed outlier: 3.537A  pdb=" N   ASP B 201 " --> pdb=" O   ASN B 198 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   LEU B 202 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 198 through 202'
    Processing helix  chain 'B' and resid 386 through 390
      removed outlier: 3.845A  pdb=" N   SER B 390 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 3.701A  pdb=" N   GLU B 483 " --> pdb=" O   ARG B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 582
      removed outlier: 4.135A  pdb=" N   GLY B 582 " --> pdb=" O   LEU B 579 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 41
      removed outlier: 6.275A  pdb=" N   GLY A  36 " --> pdb=" O   SER A  66 " (cutoff:3.500A)
      removed outlier: 5.389A  pdb=" N   SER A  66 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ARG A  62 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48
    Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48
    Processing sheet with id=AA4, first strand: chain 'A' and resid 56 through 59
    Processing sheet with id=AA5, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 147
      removed outlier: 6.303A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA A 230 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ALA A 145 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   GLU A 232 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   SER A 206 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 147
      removed outlier: 6.303A  pdb=" N   VAL A 143 " --> pdb=" O   ASN A 228 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA A 230 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ALA A 145 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.999A  pdb=" N   GLU A 232 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   GLU A 147 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153
    Processing sheet with id=AA9, first strand: chain 'A' and resid 248 through 252
      removed outlier: 6.142A  pdb=" N   THR A 249 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   GLN A 324 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 324 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 257 through 260
    Processing sheet with id=AB2, first strand: chain 'A' and resid 328 through 331
      removed outlier: 6.828A  pdb=" N   ALA A 349 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 339
      removed outlier: 6.499A  pdb=" N   THR A 336 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   GLN A 413 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA A 338 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A 398 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 344 through 346
    Processing sheet with id=AB5, first strand: chain 'A' and resid 415 through 418
      removed outlier: 3.656A  pdb=" N   ALA A 445 " --> pdb=" O   LEU A 415 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ARG A 443 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 427 through 431
    Processing sheet with id=AB7, first strand: chain 'A' and resid 435 through 439
    Processing sheet with id=AB8, first strand: chain 'A' and resid 510 through 513
      removed outlier: 6.687A  pdb=" N   HIS A 531 " --> pdb=" O   THR A 512 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 518 through 519
    Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 528
    Processing sheet with id=AC2, first strand: chain 'B' and resid 35 through 41
      removed outlier: 6.202A  pdb=" N   GLY B  36 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
      removed outlier: 5.297A  pdb=" N   SER B  66 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   ARG B  62 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 46 through 48
      removed outlier: 3.551A  pdb=" N   THR B  78 " --> pdb=" O   MET B  75 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 46 through 48
    Processing sheet with id=AC5, first strand: chain 'B' and resid 56 through 59
    Processing sheet with id=AC6, first strand: chain 'B' and resid 131 through 132
      removed outlier: 3.516A  pdb=" N   PHE B 131 " --> pdb=" O   TYR B 161 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 143 through 147
      removed outlier: 6.295A  pdb=" N   VAL B 143 " --> pdb=" O   ASN B 228 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   ALA B 230 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   ALA B 145 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   GLU B 232 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   GLU B 147 " --> pdb=" O   GLU B 232 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 153
    Processing sheet with id=AC9, first strand: chain 'B' and resid 165 through 168
    Processing sheet with id=AD1, first strand: chain 'B' and resid 241 through 244
    Processing sheet with id=AD2, first strand: chain 'B' and resid 248 through 251
    Processing sheet with id=AD3, first strand: chain 'B' and resid 328 through 331
      removed outlier: 6.749A  pdb=" N   ALA B 349 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 336 through 339
      removed outlier: 6.573A  pdb=" N   THR B 336 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   GLN B 413 " --> pdb=" O   THR B 336 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA B 338 " --> pdb=" O   GLN B 413 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR B 357 " --> pdb=" O   GLU B 398 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 344 through 346
    Processing sheet with id=AD6, first strand: chain 'B' and resid 415 through 418
      removed outlier: 3.656A  pdb=" N   ALA B 445 " --> pdb=" O   LEU B 415 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ARG B 443 " --> pdb=" O   PRO B 417 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 427 through 431
      removed outlier: 6.539A  pdb=" N   ILE B 428 " --> pdb=" O   SER B 504 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ARG B 506 " --> pdb=" O   ILE B 428 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   ALA B 430 " --> pdb=" O   ARG B 506 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'B' and resid 435 through 439
    Processing sheet with id=AD9, first strand: chain 'B' and resid 510 through 513
      removed outlier: 6.783A  pdb=" N   HIS B 531 " --> pdb=" O   THR B 512 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'B' and resid 518 through 519
      removed outlier: 3.550A  pdb=" N   LEU B 603 " --> pdb=" O   ALA B 518 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'B' and resid 526 through 528

    316 hydrogen bonds defined for protein.
    723 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: 1.80

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2901
        1.34 -     1.46: 2109
        1.46 -     1.58: 4148
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 9218
  Sorted by residual:
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.558 -0.152 2.00e-02 2.50e+03 5.77e+01
  bond pdb=" C1  NAG B 702 "
       pdb=" O5  NAG B 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.558 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" C1  NAG B 705 "
       pdb=" O5  NAG B 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.544 -0.138 2.00e-02 2.50e+03 4.74e+01
  bond pdb=" C1  NAG B 701 "
       pdb=" O5  NAG B 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.543 -0.137 2.00e-02 2.50e+03 4.68e+01
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.542 -0.136 2.00e-02 2.50e+03 4.62e+01
  ... (remaining 9213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.60: 12218
        3.60 -     7.21: 295
        7.21 -    10.81: 22
       10.81 -    14.42: 3
       14.42 -    18.02: 2
  Bond angle restraints: 12540
  Sorted by residual:
  angle pdb=" CG1 VAL B  91 "
        pdb=" CB  VAL B  91 "
        pdb=" CG2 VAL B  91 "
      ideal   model   delta    sigma   weight residual
     110.80   99.34   11.46 2.20e+00 2.07e-01 2.71e+01
  angle pdb=" CA  LEU A 376 "
        pdb=" CB  LEU A 376 "
        pdb=" CG  LEU A 376 "
      ideal   model   delta    sigma   weight residual
     116.30  134.32  -18.02 3.50e+00 8.16e-02 2.65e+01
  angle pdb=" C   VAL A  91 "
        pdb=" CA  VAL A  91 "
        pdb=" CB  VAL A  91 "
      ideal   model   delta    sigma   weight residual
     112.45  118.70   -6.25 1.24e+00 6.50e-01 2.54e+01
  angle pdb=" CA  LEU B 376 "
        pdb=" CB  LEU B 376 "
        pdb=" CG  LEU B 376 "
      ideal   model   delta    sigma   weight residual
     116.30  133.57  -17.27 3.50e+00 8.16e-02 2.43e+01
  angle pdb=" C   ASP B 547 "
        pdb=" N   ASP B 548 "
        pdb=" CA  ASP B 548 "
      ideal   model   delta    sigma   weight residual
     122.07  128.85   -6.78 1.43e+00 4.89e-01 2.25e+01
  ... (remaining 12535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 5246
       17.19 -    34.37: 365
       34.37 -    51.55: 83
       51.55 -    68.74: 15
       68.74 -    85.92: 7
  Dihedral angle restraints: 5716
    sinusoidal: 2418
      harmonic: 3298
  Sorted by residual:
  dihedral pdb=" CA  ARG B 425 "
           pdb=" C   ARG B 425 "
           pdb=" N   ARG B 426 "
           pdb=" CA  ARG B 426 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.50  -31.50     0      5.00e+00 4.00e-02 3.97e+01
  dihedral pdb=" CA  MET B  98 "
           pdb=" C   MET B  98 "
           pdb=" N   ASN B  99 "
           pdb=" CA  ASN B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.12  -29.88     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  ARG B 355 "
           pdb=" C   ARG B 355 "
           pdb=" N   PRO B 356 "
           pdb=" CA  PRO B 356 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.95  -27.05     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 5713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1138
       0.077 -    0.155: 233
       0.155 -    0.232: 39
       0.232 -    0.310: 11
       0.310 -    0.387: 5
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  ILE B 404 "
            pdb=" CA  ILE B 404 "
            pdb=" CG1 ILE B 404 "
            pdb=" CG2 ILE B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" CB  VAL B 108 "
            pdb=" CA  VAL B 108 "
            pdb=" CG1 VAL B 108 "
            pdb=" CG2 VAL B 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.26   -0.37 2.00e-01 2.50e+01 3.39e+00
  chirality pdb=" CB  THR B 466 "
            pdb=" CA  THR B 466 "
            pdb=" OG1 THR B 466 "
            pdb=" CG2 THR B 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.22    0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 1423 not shown)

  Planarity restraints: 1644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 461 "    0.039 2.00e-02 2.50e+03   3.58e-02 1.60e+01
        pdb=" CG  ASN B 461 "   -0.053 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 461 "    0.008 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 461 "   -0.029 2.00e-02 2.50e+03
        pdb=" C1  NAG B 703 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 115 "   -0.066 5.00e-02 4.00e+02   9.95e-02 1.58e+01
        pdb=" N   PRO B 116 "    0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 115 "    0.060 5.00e-02 4.00e+02   9.12e-02 1.33e+01
        pdb=" N   PRO A 116 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 116 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 116 "    0.051 5.00e-02 4.00e+02
  ... (remaining 1641 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 3127
        2.89 -     3.39: 6293
        3.39 -     3.90: 15071
        3.90 -     4.40: 14943
        4.40 -     4.90: 27349
  Nonbonded interactions: 66783
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 591 "
            pdb=" OD1 ASP B 594 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" OG1 THR A 591 "
            pdb=" OD1 ASP A 594 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" OG1 THR B 563 "
            pdb=" OG1 THR B 573 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" OG  SER A 136 "
            pdb=" OE1 GLU A 138 "
     model   vdw
     2.413 3.040
  nonbonded pdb=" OG  SER B 136 "
            pdb=" OE1 GLU B 138 "
     model   vdw
     2.414 3.040
  ... (remaining 66778 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: 0.02
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:             2.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.500
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5751
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      :  0.011   0.152   9240  Z= 0.491
  Angle     :  1.322  18.628  12594  Z= 0.693
  Chirality :  0.070   0.387   1426
  Planarity :  0.010   0.100   1634
  Dihedral  : 12.938  85.924   3552
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.23), residues: 1142
  helix:  None (None), residues: 0
  sheet: -0.31 (0.20), residues: 594
  loop : -1.64 (0.24), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 425 
 TYR   0.034   0.003   TYR B 393 
 PHE   0.031   0.003   PHE A 493 
 TRP   0.039   0.003   TRP A 346 
 HIS   0.014   0.002   HIS B 534 

Details of bonding type rmsd
  covalent geometry    : bond        0.01097 ( 9218)
  covalent geometry    : angle       1.26360 (12540)
  SS BOND              : bond        0.00797 (   12)
  SS BOND              : angle       1.50488 (   24)
  hydrogen bonds       : bond        0.14373 (  300)
  hydrogen bonds       : angle       6.84478 (  723)
  link_NAG-ASN         : bond        0.01531 (   10)
  link_NAG-ASN         : angle       8.04958 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 ASN cc_start: 0.5727 (m110) cc_final: 0.5387 (m110)
REVERT: A  328 GLU cc_start: 0.6397 (mp0) cc_final: 0.6063 (mp0)
REVERT: A  359 ARG cc_start: 0.7784 (tmm160) cc_final: 0.7388 (ttp-110)
REVERT: B   75 MET cc_start: 0.7015 (ttt) cc_final: 0.6617 (ttt)
REVERT: B  367 LEU cc_start: 0.4956 (tp) cc_final: 0.4151 (tp)
REVERT: B  409 GLU cc_start: 0.7198 (tt0) cc_final: 0.6951 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1287
  time to fit residues: 21.5530
Evaluate side-chains
  116 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0270
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
A 324 GLN
A 326 GLN
B 104 GLN
** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.257743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.224059 restraints weight = 12697.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.222040 restraints weight = 18310.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.224813 restraints weight = 14237.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.224643 restraints weight = 9358.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.225485 restraints weight = 9115.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5745
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9240  Z= 0.151
  Angle     :  0.628  12.496  12594  Z= 0.310
  Chirality :  0.043   0.205   1426
  Planarity :  0.006   0.063   1634
  Dihedral  :  5.817  36.015   1450
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  :  5.72 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.24), residues: 1142
  helix: -5.25 (0.23), residues: 12
  sheet:  0.08 (0.20), residues: 582
  loop : -1.16 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 425 
 TYR   0.009   0.001   TYR B 405 
 PHE   0.011   0.001   PHE A 245 
 TRP   0.018   0.001   TRP A 346 
 HIS   0.005   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9218)
  covalent geometry    : angle       0.58585 (12540)
  SS BOND              : bond        0.00494 (   12)
  SS BOND              : angle       0.71586 (   24)
  hydrogen bonds       : bond        0.03091 (  300)
  hydrogen bonds       : angle       5.47064 (  723)
  link_NAG-ASN         : bond        0.00799 (   10)
  link_NAG-ASN         : angle       4.66168 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3300 (mpp) cc_final: 0.2591 (pmm)
REVERT: A  255 GLN cc_start: 0.6981 (mp10) cc_final: 0.6706 (mp10)
REVERT: B  109 TYR cc_start: 0.7053 (m-80) cc_final: 0.6817 (m-80)
REVERT: B  459 LEU cc_start: 0.8137 (mt) cc_final: 0.7924 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 129
  average time/residue: 0.1297
  time to fit residues: 21.9278
Evaluate side-chains
  115 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain B residue  390 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    7.9990
   chunk 111 optimal weight:    7.9990
   chunk 45 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0030
   chunk 105 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
A 324 GLN
** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4819 r_free = 0.4819 target = 0.252121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.216689 restraints weight = 12411.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.215456 restraints weight = 16520.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.217990 restraints weight = 14437.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.217958 restraints weight = 9543.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.218868 restraints weight = 8842.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5800
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9240  Z= 0.179
  Angle     :  0.609  11.693  12594  Z= 0.300
  Chirality :  0.043   0.171   1426
  Planarity :  0.005   0.058   1634
  Dihedral  :  5.195  32.574   1450
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  8.52 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.24), residues: 1142
  helix: -5.32 (0.20), residues: 12
  sheet:  0.24 (0.21), residues: 572
  loop : -0.83 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 345 
 TYR   0.012   0.001   TYR A 486 
 PHE   0.013   0.001   PHE B 245 
 TRP   0.015   0.001   TRP B 346 
 HIS   0.005   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 9218)
  covalent geometry    : angle       0.57100 (12540)
  SS BOND              : bond        0.00645 (   12)
  SS BOND              : angle       0.84949 (   24)
  hydrogen bonds       : bond        0.03084 (  300)
  hydrogen bonds       : angle       5.44429 (  723)
  link_NAG-ASN         : bond        0.00655 (   10)
  link_NAG-ASN         : angle       4.31395 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3690 (mpp) cc_final: 0.2674 (pmm)
REVERT: B  365 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.6027 (pt0)
  outliers start: 10
  outliers final: 7
  residues processed: 124
  average time/residue: 0.1362
  time to fit residues: 21.8562
Evaluate side-chains
  126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  588 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  365 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 104 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  94 ASN
A 324 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.256098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.220318 restraints weight = 11895.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.220698 restraints weight = 18369.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.221723 restraints weight = 15211.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.220590 restraints weight = 11519.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.221624 restraints weight = 10659.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5882
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.083   9240  Z= 0.307
  Angle     :  0.694  11.361  12594  Z= 0.344
  Chirality :  0.046   0.193   1426
  Planarity :  0.005   0.058   1634
  Dihedral  :  5.466  29.771   1450
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.88 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.25), residues: 1142
  helix: -5.38 (0.18), residues: 12
  sheet:  0.14 (0.21), residues: 566
  loop : -0.73 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 359 
 TYR   0.014   0.002   TYR A 486 
 PHE   0.018   0.001   PHE A 245 
 TRP   0.014   0.002   TRP B  73 
 HIS   0.008   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 ( 9218)
  covalent geometry    : angle       0.66193 (12540)
  SS BOND              : bond        0.01100 (   12)
  SS BOND              : angle       1.32529 (   24)
  hydrogen bonds       : bond        0.03615 (  300)
  hydrogen bonds       : angle       6.01138 (  723)
  link_NAG-ASN         : bond        0.00820 (   10)
  link_NAG-ASN         : angle       4.20041 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3595 (mpp) cc_final: 0.2882 (pmm)
REVERT: A  482 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5881 (t0)
REVERT: B   75 MET cc_start: 0.6725 (ttt) cc_final: 0.6456 (ttt)
REVERT: B   80 MET cc_start: 0.5906 (ppp) cc_final: 0.4544 (ptt)
REVERT: B  485 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7726 (mtpp)
  outliers start: 17
  outliers final: 12
  residues processed: 114
  average time/residue: 0.1372
  time to fit residues: 20.2573
Evaluate side-chains
  120 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  326 GLN
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  485 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0770
   chunk 53 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 94 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0970
   chunk 20 optimal weight:    0.2980
   chunk 83 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.2334

-------------------------------------------------------------------------------
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 = 0.4854 r_free = 0.4854 target = 0.255415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.222431 restraints weight = 12597.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.221441 restraints weight = 17779.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.223241 restraints weight = 13890.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.223498 restraints weight = 8965.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.223745 restraints weight = 8634.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.4506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5784
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9240  Z= 0.109
  Angle     :  0.558  10.154  12594  Z= 0.275
  Chirality :  0.042   0.151   1426
  Planarity :  0.004   0.044   1634
  Dihedral  :  4.803  31.199   1450
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.43 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.25), residues: 1142
  helix: -5.35 (0.19), residues: 12
  sheet:  0.31 (0.22), residues: 536
  loop : -0.61 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 359 
 TYR   0.010   0.001   TYR A 486 
 PHE   0.009   0.001   PHE B 245 
 TRP   0.009   0.001   TRP A 360 
 HIS   0.002   0.000   HIS B 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9218)
  covalent geometry    : angle       0.52772 (12540)
  SS BOND              : bond        0.00267 (   12)
  SS BOND              : angle       0.39533 (   24)
  hydrogen bonds       : bond        0.02722 (  300)
  hydrogen bonds       : angle       5.21968 (  723)
  link_NAG-ASN         : bond        0.00642 (   10)
  link_NAG-ASN         : angle       3.79611 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3768 (mpp) cc_final: 0.3252 (pmm)
REVERT: B  485 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7639 (mtpp)
  outliers start: 13
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1486
  time to fit residues: 23.9007
Evaluate side-chains
  126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  479 SER
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 6 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0370
   chunk 16 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A 324 GLN
B 521 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.253810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.217271 restraints weight = 12497.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.215616 restraints weight = 16659.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.218670 restraints weight = 13074.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.218333 restraints weight = 9086.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.219147 restraints weight = 8759.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.4458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5882
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9240  Z= 0.196
  Angle     :  0.602  10.744  12594  Z= 0.296
  Chirality :  0.043   0.168   1426
  Planarity :  0.004   0.044   1634
  Dihedral  :  4.922  31.083   1450
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 11.85 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.25), residues: 1142
  helix: -5.32 (0.20), residues: 12
  sheet:  0.32 (0.22), residues: 538
  loop : -0.56 (0.26), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 359 
 TYR   0.016   0.001   TYR A 486 
 PHE   0.013   0.001   PHE A 245 
 TRP   0.011   0.001   TRP B  73 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 9218)
  covalent geometry    : angle       0.57270 (12540)
  SS BOND              : bond        0.00625 (   12)
  SS BOND              : angle       0.76771 (   24)
  hydrogen bonds       : bond        0.02993 (  300)
  hydrogen bonds       : angle       5.41943 (  723)
  link_NAG-ASN         : bond        0.00647 (   10)
  link_NAG-ASN         : angle       3.79595 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3554 (mpp) cc_final: 0.2946 (pmm)
REVERT: A  465 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7129 (m)
REVERT: A  482 ASP cc_start: 0.6516 (t0) cc_final: 0.6268 (t70)
REVERT: B  485 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7673 (mtpp)
  outliers start: 16
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1418
  time to fit residues: 21.7161
Evaluate side-chains
  126 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 48 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 96 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0170
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
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 = 0.4848 r_free = 0.4848 target = 0.257933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.221663 restraints weight = 12230.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.212930 restraints weight = 12868.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.214610 restraints weight = 12965.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.216170 restraints weight = 9461.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.216401 restraints weight = 8300.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6100
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9240  Z= 0.179
  Angle     :  0.591  12.121  12594  Z= 0.290
  Chirality :  0.043   0.162   1426
  Planarity :  0.004   0.040   1634
  Dihedral  :  4.898  32.098   1450
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.16 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.25), residues: 1142
  helix: -5.30 (0.22), residues: 12
  sheet:  0.26 (0.22), residues: 536
  loop : -0.51 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 359 
 TYR   0.015   0.001   TYR A 486 
 PHE   0.012   0.001   PHE B 245 
 TRP   0.014   0.001   TRP B  73 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 9218)
  covalent geometry    : angle       0.56439 (12540)
  SS BOND              : bond        0.00568 (   12)
  SS BOND              : angle       0.66498 (   24)
  hydrogen bonds       : bond        0.02873 (  300)
  hydrogen bonds       : angle       5.40602 (  723)
  link_NAG-ASN         : bond        0.00616 (   10)
  link_NAG-ASN         : angle       3.63858 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.4112 (mpp) cc_final: 0.3331 (pmm)
REVERT: A  465 VAL cc_start: 0.7374 (OUTLIER) cc_final: 0.7162 (m)
REVERT: A  482 ASP cc_start: 0.6517 (t0) cc_final: 0.6266 (t0)
REVERT: B   80 MET cc_start: 0.5585 (ppp) cc_final: 0.4291 (ptt)
REVERT: B  357 THR cc_start: 0.7797 (t) cc_final: 0.7555 (p)
REVERT: B  376 LEU cc_start: 0.6172 (tp) cc_final: 0.5944 (tp)
REVERT: B  457 GLU cc_start: 0.7241 (pp20) cc_final: 0.6717 (pt0)
REVERT: B  485 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7867 (mtpp)
  outliers start: 21
  outliers final: 17
  residues processed: 126
  average time/residue: 0.1367
  time to fit residues: 22.1638
Evaluate side-chains
  133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 77 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0970
   chunk 84 optimal weight:    0.4980
   chunk 88 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 24 optimal weight:    0.3980
   chunk 94 optimal weight:    0.3980
   chunk 106 optimal weight:    0.5980
   overall best weight:    0.2978

-------------------------------------------------------------------------------
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 = 0.4885 r_free = 0.4885 target = 0.260569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.225889 restraints weight = 12460.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.225487 restraints weight = 17031.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.226832 restraints weight = 15528.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.226606 restraints weight = 10064.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.227278 restraints weight = 9694.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5819
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9240  Z= 0.121
  Angle     :  0.565  13.318  12594  Z= 0.276
  Chirality :  0.042   0.169   1426
  Planarity :  0.004   0.041   1634
  Dihedral  :  4.684  33.739   1450
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.58 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.25), residues: 1142
  helix: -5.29 (0.22), residues: 12
  sheet:  0.34 (0.22), residues: 534
  loop : -0.44 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 359 
 TYR   0.024   0.001   TYR B 109 
 PHE   0.009   0.001   PHE B 245 
 TRP   0.010   0.001   TRP B  73 
 HIS   0.003   0.000   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9218)
  covalent geometry    : angle       0.54022 (12540)
  SS BOND              : bond        0.00345 (   12)
  SS BOND              : angle       0.43518 (   24)
  hydrogen bonds       : bond        0.02652 (  300)
  hydrogen bonds       : angle       5.12799 (  723)
  link_NAG-ASN         : bond        0.00566 (   10)
  link_NAG-ASN         : angle       3.41842 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3717 (mpp) cc_final: 0.3312 (pmm)
REVERT: A  328 GLU cc_start: 0.6218 (mp0) cc_final: 0.5925 (mt-10)
REVERT: A  465 VAL cc_start: 0.7348 (t) cc_final: 0.7070 (m)
REVERT: A  482 ASP cc_start: 0.6502 (t0) cc_final: 0.6264 (t0)
REVERT: B  109 TYR cc_start: 0.7010 (m-80) cc_final: 0.6595 (m-80)
REVERT: B  376 LEU cc_start: 0.6101 (tp) cc_final: 0.5822 (tp)
REVERT: B  485 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7488 (mtpp)
  outliers start: 17
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1428
  time to fit residues: 21.8175
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  483 GLU
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  333 ILE
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 92 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 226 GLN
A 228 ASN
B 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.256999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.221477 restraints weight = 11976.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.219791 restraints weight = 16732.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.221265 restraints weight = 14598.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.220782 restraints weight = 10912.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.221771 restraints weight = 9288.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5931
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.089   9240  Z= 0.324
  Angle     :  0.704  13.643  12594  Z= 0.345
  Chirality :  0.046   0.214   1426
  Planarity :  0.004   0.040   1634
  Dihedral  :  5.272  31.635   1450
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.16 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.25), residues: 1142
  helix: -5.33 (0.20), residues: 12
  sheet: -0.01 (0.22), residues: 524
  loop : -0.56 (0.26), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 359 
 TYR   0.024   0.002   TYR B 109 
 PHE   0.017   0.001   PHE A 245 
 TRP   0.014   0.002   TRP B  73 
 HIS   0.007   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00768 ( 9218)
  covalent geometry    : angle       0.68111 (12540)
  SS BOND              : bond        0.01029 (   12)
  SS BOND              : angle       1.13641 (   24)
  hydrogen bonds       : bond        0.03467 (  300)
  hydrogen bonds       : angle       5.89501 (  723)
  link_NAG-ASN         : bond        0.00761 (   10)
  link_NAG-ASN         : angle       3.62689 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.3758 (mpp) cc_final: 0.3435 (pmm)
REVERT: A  328 GLU cc_start: 0.6313 (mp0) cc_final: 0.5958 (mt-10)
REVERT: A  482 ASP cc_start: 0.6554 (t0) cc_final: 0.6269 (t0)
REVERT: B   80 MET cc_start: 0.6000 (ppp) cc_final: 0.4695 (ptt)
REVERT: B  435 GLU cc_start: 0.5762 (tm-30) cc_final: 0.5526 (tm-30)
REVERT: B  474 ILE cc_start: 0.8203 (mt) cc_final: 0.7865 (mt)
REVERT: B  485 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7730 (mtpp)
REVERT: B  539 ASP cc_start: 0.6813 (t0) cc_final: 0.6428 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1401
  time to fit residues: 21.9878
Evaluate side-chains
  128 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  465 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  346 TRP
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Chi-restraints excluded: chain B residue  590 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 79 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 85 optimal weight:    0.0170
   chunk 106 optimal weight:    0.8980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.4876 r_free = 0.4876 target = 0.259384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.226121 restraints weight = 12096.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.224426 restraints weight = 17826.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.226390 restraints weight = 14611.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.226270 restraints weight = 10334.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.226877 restraints weight = 9376.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.4477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5836
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9240  Z= 0.195
  Angle     :  0.618  14.524  12594  Z= 0.303
  Chirality :  0.044   0.186   1426
  Planarity :  0.004   0.041   1634
  Dihedral  :  5.049  34.033   1450
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.68 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.25), residues: 1142
  helix: -5.29 (0.22), residues: 12
  sheet:  0.19 (0.23), residues: 540
  loop : -0.48 (0.27), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 425 
 TYR   0.034   0.002   TYR B 109 
 PHE   0.012   0.001   PHE B 245 
 TRP   0.010   0.001   TRP B  73 
 HIS   0.003   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 9218)
  covalent geometry    : angle       0.59540 (12540)
  SS BOND              : bond        0.00621 (   12)
  SS BOND              : angle       0.69889 (   24)
  hydrogen bonds       : bond        0.02987 (  300)
  hydrogen bonds       : angle       5.58675 (  723)
  link_NAG-ASN         : bond        0.00591 (   10)
  link_NAG-ASN         : angle       3.39142 (   30)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  381 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6603 (mpp80)
REVERT: A  482 ASP cc_start: 0.6581 (t0) cc_final: 0.6332 (t0)
REVERT: B   80 MET cc_start: 0.5775 (ppp) cc_final: 0.4460 (ptt)
REVERT: B  376 LEU cc_start: 0.6145 (tp) cc_final: 0.5882 (tp)
REVERT: B  485 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7666 (mtpp)
  outliers start: 15
  outliers final: 13
  residues processed: 122
  average time/residue: 0.1408
  time to fit residues: 22.0504
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  346 TRP
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  513 LEU
Chi-restraints excluded: chain B residue  115 ASN
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  365 GLU
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  485 LYS
Chi-restraints excluded: chain B residue  587 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 102 optimal weight:    0.8980
   chunk 93 optimal weight:    0.4980
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 228 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.258452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.223809 restraints weight = 11966.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.221457 restraints weight = 17456.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.224049 restraints weight = 16092.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.223704 restraints weight = 10366.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.224405 restraints weight = 10044.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5868
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9240  Z= 0.187
  Angle     :  0.614  14.262  12594  Z= 0.301
  Chirality :  0.044   0.196   1426
  Planarity :  0.004   0.041   1634
  Dihedral  :  4.968  33.921   1450
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.68 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.25), residues: 1142
  helix: -5.28 (0.23), residues: 12
  sheet:  0.15 (0.22), residues: 544
  loop : -0.43 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 359 
 TYR   0.028   0.002   TYR B 109 
 PHE   0.012   0.001   PHE B 245 
 TRP   0.009   0.001   TRP A 346 
 HIS   0.003   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 9218)
  covalent geometry    : angle       0.59301 (12540)
  SS BOND              : bond        0.00599 (   12)
  SS BOND              : angle       0.68021 (   24)
  hydrogen bonds       : bond        0.02923 (  300)
  hydrogen bonds       : angle       5.49418 (  723)
  link_NAG-ASN         : bond        0.00571 (   10)
  link_NAG-ASN         : angle       3.27376 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1709.42 seconds
wall clock time: 30 minutes 14.20 seconds (1814.20 seconds total)