Starting phenix.real_space_refine
on Wed Sep 17 09:43:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vly_43348/09_2025/8vly_43348.map"
  }
  resolution = 3.61
  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=   0.001 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5148      2.51       5
     N    1217      2.21       5
     O    1354      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 7755
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3834
          Classifications: {'peptide': 497}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 23, 'TRANS': 473}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 60
    Chain: "B"
      Number of atoms: 3823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 495, 3823
          Classifications: {'peptide': 495}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 23, 'TRANS': 471}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 53
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 2.02, per 1000 atoms: 0.26
  Number of scatterers: 7755
  At special positions: 0
  Unit cell: (87.57, 112.59, 100.914, 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      36     16.00
     O    1354      8.00
     N    1217      7.00
     C    5148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 362 " - pdb=" SG  CYS B 362 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A 162 "
      " NAG A 702 " - " ASN A  94 "
      " NAG B 701 " - " ASN B 162 "
      " NAG B 702 " - " ASN B  94 "
      " NAG B 703 " - " ASN B 142 "
      " NAG C   1 " - " ASN A 142 "
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 515.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      53.6% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 269 through 288
      removed outlier: 3.609A  pdb=" N   GLY A 288 " --> pdb=" O   PHE A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
    Processing helix  chain 'A' and resid 308 through 332
      removed outlier: 3.789A  pdb=" N   TRP A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 357
      removed outlier: 3.551A  pdb=" N   LEU A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 371
      removed outlier: 3.695A  pdb=" N   VAL A 371 " --> pdb=" O   TRP A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 417 through 438
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 465 through 476
    Processing helix  chain 'A' and resid 486 through 491
      removed outlier: 3.537A  pdb=" N   HIS A 491 " --> pdb=" O   ALA A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 524
      removed outlier: 4.119A  pdb=" N   ILE A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ASN A 506 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 551
      removed outlier: 3.661A  pdb=" N   ILE A 531 " --> pdb=" O   ARG A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 600 through 606
      removed outlier: 3.719A  pdb=" N   GLY A 604 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 620 through 624
    Processing helix  chain 'A' and resid 632 through 657
    Processing helix  chain 'B' and resid 269 through 287
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.655A  pdb=" N   TYR B 292 " --> pdb=" O   GLY B 289 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   LYS B 296 " --> pdb=" O   TRP B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'B' and resid 309 through 332
    Processing helix  chain 'B' and resid 334 through 356
      removed outlier: 3.534A  pdb=" N   LEU B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.528A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 458
      removed outlier: 3.659A  pdb=" N   LYS B 458 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 476
    Processing helix  chain 'B' and resid 502 through 524
      removed outlier: 4.269A  pdb=" N   ASN B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 551
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 605
      removed outlier: 3.662A  pdb=" N   GLY B 604 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
      removed outlier: 3.631A  pdb=" N   HIS B 636 " --> pdb=" O   SER B 632 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132
      removed outlier: 8.821A  pdb=" N   TYR A 163 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LYS A 168 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA A 178 " --> pdb=" O   LYS A 168 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.179A  pdb=" N   VAL A 111 " --> pdb=" O   TRP A  99 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   TRP A  99 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   VAL A 113 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU A 139 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ARG A 152 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 126 through 127
      removed outlier: 3.776A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL B 167 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 132
      removed outlier: 3.776A  pdb=" N   HIS B  87 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL B 167 " --> pdb=" O   HIS B  87 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 115
      removed outlier: 5.584A  pdb=" N   VAL B 111 " --> pdb=" O   TRP B  99 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   TRP B  99 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B 113 " --> pdb=" O   VAL B  97 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   THR B  96 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ASN B 142 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   SER B 137 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   GLU B 154 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   LEU B 139 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   ARG B 152 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU B 141 " --> pdb=" O   VAL B 150 " (cutoff:3.500A)

    422 hydrogen bonds defined for protein.
    1209 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: 1.28

  Time building geometry restraints manager: 0.96 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: 2307
        1.34 -     1.46: 1540
        1.46 -     1.58: 4084
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 7979
  Sorted by residual:
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C   TRP A 418 "
       pdb=" N   PRO A 419 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.07e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.440 -0.034 2.00e-02 2.50e+03 2.88e+00
  bond pdb=" C1  NAG B 701 "
       pdb=" O5  NAG B 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.72e+00
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.95e+00
  ... (remaining 7974 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 10615
        1.38 -     2.76: 246
        2.76 -     4.14: 43
        4.14 -     5.52: 17
        5.52 -     6.90: 5
  Bond angle restraints: 10926
  Sorted by residual:
  angle pdb=" N   TRP A 418 "
        pdb=" CA  TRP A 418 "
        pdb=" C   TRP A 418 "
      ideal   model   delta    sigma   weight residual
     109.81  116.05   -6.24 2.21e+00 2.05e-01 7.98e+00
  angle pdb=" C   LYS B 551 "
        pdb=" N   VAL B 552 "
        pdb=" CA  VAL B 552 "
      ideal   model   delta    sigma   weight residual
     121.97  126.42   -4.45 1.80e+00 3.09e-01 6.10e+00
  angle pdb=" CG  ARG B 269 "
        pdb=" CD  ARG B 269 "
        pdb=" NE  ARG B 269 "
      ideal   model   delta    sigma   weight residual
     112.00  106.58    5.42 2.20e+00 2.07e-01 6.06e+00
  angle pdb=" CB  MET B 325 "
        pdb=" CG  MET B 325 "
        pdb=" SD  MET B 325 "
      ideal   model   delta    sigma   weight residual
     112.70  119.42   -6.72 3.00e+00 1.11e-01 5.02e+00
  angle pdb=" C   LEU A 268 "
        pdb=" N   ARG A 269 "
        pdb=" CA  ARG A 269 "
      ideal   model   delta    sigma   weight residual
     121.54  125.61   -4.07 1.91e+00 2.74e-01 4.55e+00
  ... (remaining 10921 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4072
       17.53 -    35.06: 420
       35.06 -    52.59: 111
       52.59 -    70.12: 21
       70.12 -    87.65: 5
  Dihedral angle restraints: 4629
    sinusoidal: 1769
      harmonic: 2860
  Sorted by residual:
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 462 "
           pdb=" CB  CYS A 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.14  -73.14     1      1.00e+01 1.00e-02 6.82e+01
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.41  -65.41     1      1.00e+01 1.00e-02 5.61e+01
  dihedral pdb=" CB  CYS A 104 "
           pdb=" SG  CYS A 104 "
           pdb=" SG  CYS A 107 "
           pdb=" CB  CYS A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -50.30  -35.70     1      1.00e+01 1.00e-02 1.80e+01
  ... (remaining 4626 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1033
       0.050 -    0.100: 224
       0.100 -    0.150: 30
       0.150 -    0.200: 2
       0.200 -    0.249: 1
  Chirality restraints: 1290
  Sorted by residual:
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A  94 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  THR A 383 "
            pdb=" CA  THR A 383 "
            pdb=" OG1 THR A 383 "
            pdb=" CG2 THR A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.12e-01
  chirality pdb=" CB  VAL B 552 "
            pdb=" CA  VAL B 552 "
            pdb=" CG1 VAL B 552 "
            pdb=" CG2 VAL B 552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1287 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 269 "   -0.171 9.50e-02 1.11e+02   7.69e-02 3.76e+00
        pdb=" NE  ARG B 269 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 269 "    0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 269 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 269 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 269 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   ARG B 269 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ARG B 269 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER B 270 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 274 "   -0.008 2.00e-02 2.50e+03   1.11e-02 2.15e+00
        pdb=" CG  PHE B 274 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 274 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 274 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 274 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 274 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 274 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 310
        2.72 -     3.27: 7942
        3.27 -     3.81: 12991
        3.81 -     4.36: 14477
        4.36 -     4.90: 26113
  Nonbonded interactions: 61833
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 147 "
            pdb=" O6  NAG C   1 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   ILE A 355 "
            pdb=" OH  TYR A 361 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" NH1 ARG A 275 "
            pdb=" O   GLY A 604 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   ILE B 355 "
            pdb=" OH  TYR B 361 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   PRO A 116 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.278 3.040
  ... (remaining 61828 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 76 through 144 or (resid 145 through 146 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 147 through 170 or resid 177 th \ 
rough 189 or resid 268 through 330 or (resid 331 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 332 through 476 or (resid 477 through 478 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 479 through 492 o \ 
r (resid 493 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 
94 through 526 or (resid 527 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 528 through 550 or (resid 551 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 552 through 555 or (resid 556 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 557 through 660 or resid 701 thro \ 
ugh 702))
  selection = (chain 'B' and (resid 76 through 116 or (resid 117 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 118 through 168 or (resid 169 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 170 through 179 or (resid 1 \ 
80 and (name N or name CA or name C or name O or name CB )) or resid 181 through \ 
 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 346 through 407 or resid 411 through 477 or (resid 478 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 479 through 524 or (resid 525 thro \ 
ugh 527 and (name N or name CA or name C or name O or name CB )) or resid 528 th \ 
rough 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 593 through 625 or (resid 626 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 627 through 655 or (resid 656 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 657 or (resid 658 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 659 through 660 or resid 702 throu \ 
gh 703))
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.600
  Find NCS groups from input model:        0.150
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
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      :  0.004   0.041   7993  Z= 0.161
  Angle     :  0.582  13.489  10961  Z= 0.286
  Chirality :  0.041   0.249   1290
  Planarity :  0.004   0.077   1330
  Dihedral  : 15.202  87.645   2780
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 11.00 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.00 (0.28), residues: 976
  helix:  2.61 (0.23), residues: 465
  sheet: -0.55 (0.49), residues: 122
  loop : -1.44 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 269 
 TYR   0.019   0.001   TYR B 384 
 PHE   0.025   0.001   PHE B 274 
 TRP   0.012   0.001   TRP A 647 
 HIS   0.007   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7979)
  covalent geometry    : angle       0.54854 (10926)
  SS BOND              : bond        0.00206 (    7)
  SS BOND              : angle       0.54178 (   14)
  hydrogen bonds       : bond        0.12038 (  418)
  hydrogen bonds       : angle       5.64020 ( 1209)
  link_BETA1-4         : bond        0.00235 (    1)
  link_BETA1-4         : angle       1.38679 (    3)
  link_NAG-ASN         : bond        0.00810 (    6)
  link_NAG-ASN         : angle       4.82643 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A   78 LYS cc_start: 0.8777 (tppt) cc_final: 0.8542 (mmmt)
REVERT: A  325 MET cc_start: 0.8374 (tmm) cc_final: 0.8040 (tmm)
REVERT: A  551 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8502 (tttp)
REVERT: B  269 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8284 (mtp85)
  outliers start: 3
  outliers final: 2
  residues processed: 74
  average time/residue: 0.1107
  time to fit residues: 10.8292
Evaluate side-chains
  72 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain B residue  151 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.1524

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

Flipped N/Q/H residues before XYZ refinement:
B 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.115510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.094571 restraints weight = 12420.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.097352 restraints weight = 6965.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.099196 restraints weight = 4813.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.100303 restraints weight = 3763.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.101123 restraints weight = 3204.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.0692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7993  Z= 0.218
  Angle     :  0.619  13.947  10961  Z= 0.310
  Chirality :  0.043   0.238   1290
  Planarity :  0.004   0.050   1330
  Dihedral  :  6.409  57.567   1201
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.38 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.80 (0.27), residues: 976
  helix:  2.31 (0.23), residues: 469
  sheet: -0.69 (0.49), residues: 117
  loop : -1.37 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 534 
 TYR   0.021   0.002   TYR B 570 
 PHE   0.022   0.002   PHE A 601 
 TRP   0.013   0.001   TRP B 647 
 HIS   0.005   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 7979)
  covalent geometry    : angle       0.58775 (10926)
  SS BOND              : bond        0.00350 (    7)
  SS BOND              : angle       0.60061 (   14)
  hydrogen bonds       : bond        0.03990 (  418)
  hydrogen bonds       : angle       4.57427 ( 1209)
  link_BETA1-4         : bond        0.00576 (    1)
  link_BETA1-4         : angle       1.51046 (    3)
  link_NAG-ASN         : bond        0.00838 (    6)
  link_NAG-ASN         : angle       4.82668 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8538 (tttt)
REVERT: B  269 ARG cc_start: 0.8806 (mmm-85) cc_final: 0.8573 (mtp85)
  outliers start: 25
  outliers final: 20
  residues processed: 99
  average time/residue: 0.0929
  time to fit residues: 12.4360
Evaluate side-chains
  86 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  151 CYS
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  584 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0770
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B 114 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.117384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.096396 restraints weight = 12100.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.099214 restraints weight = 6782.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.101077 restraints weight = 4672.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.102391 restraints weight = 3636.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.103141 restraints weight = 3054.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7993  Z= 0.141
  Angle     :  0.560  13.294  10961  Z= 0.276
  Chirality :  0.041   0.238   1290
  Planarity :  0.004   0.039   1330
  Dihedral  :  5.764  56.039   1201
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.38 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.94 (0.28), residues: 976
  helix:  2.58 (0.23), residues: 467
  sheet: -0.73 (0.48), residues: 116
  loop : -1.48 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 275 
 TYR   0.017   0.001   TYR B 570 
 PHE   0.029   0.001   PHE B 347 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.005   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7979)
  covalent geometry    : angle       0.52547 (10926)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       0.46309 (   14)
  hydrogen bonds       : bond        0.03416 (  418)
  hydrogen bonds       : angle       4.25704 ( 1209)
  link_BETA1-4         : bond        0.00468 (    1)
  link_BETA1-4         : angle       1.69662 (    3)
  link_NAG-ASN         : bond        0.00825 (    6)
  link_NAG-ASN         : angle       4.75508 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 70
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  551 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8522 (tttt)
REVERT: B   98 TYR cc_start: 0.8332 (m-80) cc_final: 0.8069 (m-80)
REVERT: B  420 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7594 (mt0)
  outliers start: 23
  outliers final: 14
  residues processed: 89
  average time/residue: 0.0989
  time to fit residues: 11.9040
Evaluate side-chains
  82 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  420 GLN
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3328 r_free = 0.3328 target = 0.113001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.091983 restraints weight = 12594.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.094675 restraints weight = 7160.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.096490 restraints weight = 4968.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.097368 restraints weight = 3912.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.098235 restraints weight = 3411.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7993  Z= 0.252
  Angle     :  0.654  14.413  10961  Z= 0.326
  Chirality :  0.044   0.231   1290
  Planarity :  0.004   0.034   1330
  Dihedral  :  5.722  52.180   1200
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 14.75 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.62 (0.27), residues: 976
  helix:  2.16 (0.23), residues: 470
  sheet: -0.85 (0.48), residues: 118
  loop : -1.43 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 269 
 TYR   0.025   0.002   TYR B 570 
 PHE   0.023   0.002   PHE A 601 
 TRP   0.013   0.001   TRP B 647 
 HIS   0.004   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 ( 7979)
  covalent geometry    : angle       0.62184 (10926)
  SS BOND              : bond        0.00421 (    7)
  SS BOND              : angle       0.74277 (   14)
  hydrogen bonds       : bond        0.04050 (  418)
  hydrogen bonds       : angle       4.46542 ( 1209)
  link_BETA1-4         : bond        0.00351 (    1)
  link_BETA1-4         : angle       1.56282 (    3)
  link_NAG-ASN         : bond        0.00829 (    6)
  link_NAG-ASN         : angle       4.98861 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 68
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 CYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7618 (m)
REVERT: B  420 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7602 (mt0)
  outliers start: 41
  outliers final: 30
  residues processed: 103
  average time/residue: 0.0938
  time to fit residues: 13.1765
Evaluate side-chains
  96 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  420 GLN
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0170
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   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 = 0.3375 r_free = 0.3375 target = 0.117617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.099493 restraints weight = 11980.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.099893 restraints weight = 8320.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.100824 restraints weight = 7414.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.101138 restraints weight = 6300.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.101502 restraints weight = 5577.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7993  Z= 0.135
  Angle     :  0.560  13.179  10961  Z= 0.277
  Chirality :  0.041   0.232   1290
  Planarity :  0.003   0.026   1330
  Dihedral  :  5.347  53.075   1200
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 16.38 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.90 (0.28), residues: 976
  helix:  2.46 (0.23), residues: 472
  sheet: -0.78 (0.48), residues: 118
  loop : -1.41 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 534 
 TYR   0.018   0.001   TYR B 570 
 PHE   0.019   0.001   PHE B 322 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.004   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7979)
  covalent geometry    : angle       0.52499 (10926)
  SS BOND              : bond        0.00262 (    7)
  SS BOND              : angle       0.59280 (   14)
  hydrogen bonds       : bond        0.03362 (  418)
  hydrogen bonds       : angle       4.19186 ( 1209)
  link_BETA1-4         : bond        0.00347 (    1)
  link_BETA1-4         : angle       1.82050 (    3)
  link_NAG-ASN         : bond        0.00794 (    6)
  link_NAG-ASN         : angle       4.76831 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 CYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7428 (m)
REVERT: B  420 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7651 (mt0)
  outliers start: 37
  outliers final: 29
  residues processed: 105
  average time/residue: 0.0934
  time to fit residues: 13.2608
Evaluate side-chains
  100 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  321 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  420 GLN
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 75 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 516 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.114773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.093675 restraints weight = 12503.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.096460 restraints weight = 7055.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.098364 restraints weight = 4865.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.099622 restraints weight = 3778.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.100312 restraints weight = 3186.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7993  Z= 0.204
  Angle     :  0.609  13.773  10961  Z= 0.302
  Chirality :  0.042   0.232   1290
  Planarity :  0.004   0.028   1330
  Dihedral  :  5.458  52.434   1200
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 16.50 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.76 (0.27), residues: 976
  helix:  2.32 (0.23), residues: 472
  sheet: -0.82 (0.48), residues: 118
  loop : -1.44 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 534 
 TYR   0.022   0.001   TYR B 570 
 PHE   0.019   0.001   PHE A 601 
 TRP   0.029   0.001   TRP A 661 
 HIS   0.004   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 7979)
  covalent geometry    : angle       0.57524 (10926)
  SS BOND              : bond        0.00326 (    7)
  SS BOND              : angle       0.66398 (   14)
  hydrogen bonds       : bond        0.03673 (  418)
  hydrogen bonds       : angle       4.26701 ( 1209)
  link_BETA1-4         : bond        0.00240 (    1)
  link_BETA1-4         : angle       1.66609 (    3)
  link_NAG-ASN         : bond        0.00772 (    6)
  link_NAG-ASN         : angle       4.90007 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 68
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 CYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7492 (m)
REVERT: A  551 LYS cc_start: 0.8569 (tttt) cc_final: 0.8195 (tmtt)
REVERT: B  420 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7507 (mt0)
  outliers start: 40
  outliers final: 33
  residues processed: 102
  average time/residue: 0.1008
  time to fit residues: 13.9644
Evaluate side-chains
  102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 67
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  420 GLN
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.115355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.094205 restraints weight = 12327.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.096961 restraints weight = 6979.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.098831 restraints weight = 4839.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.100075 restraints weight = 3792.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.100937 restraints weight = 3188.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7993  Z= 0.169
  Angle     :  0.582  13.354  10961  Z= 0.288
  Chirality :  0.042   0.233   1290
  Planarity :  0.003   0.027   1330
  Dihedral  :  5.384  52.451   1200
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 17.50 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.82 (0.28), residues: 976
  helix:  2.39 (0.23), residues: 472
  sheet: -0.78 (0.48), residues: 118
  loop : -1.44 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 534 
 TYR   0.020   0.001   TYR B 570 
 PHE   0.017   0.001   PHE B 322 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.004   0.001   HIS B  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7979)
  covalent geometry    : angle       0.54735 (10926)
  SS BOND              : bond        0.00266 (    7)
  SS BOND              : angle       0.66508 (   14)
  hydrogen bonds       : bond        0.03523 (  418)
  hydrogen bonds       : angle       4.20221 ( 1209)
  link_BETA1-4         : bond        0.00383 (    1)
  link_BETA1-4         : angle       1.77774 (    3)
  link_NAG-ASN         : bond        0.00760 (    6)
  link_NAG-ASN         : angle       4.83469 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 69
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 CYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7491 (m)
REVERT: A  317 MET cc_start: 0.8251 (tmm) cc_final: 0.7693 (ttt)
REVERT: A  331 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7323 (ttp80)
REVERT: A  551 LYS cc_start: 0.8551 (tttt) cc_final: 0.8156 (tmtt)
REVERT: B  420 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7575 (mt0)
  outliers start: 38
  outliers final: 32
  residues processed: 102
  average time/residue: 0.0975
  time to fit residues: 13.5589
Evaluate side-chains
  100 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 66
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  420 GLN
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0670
   chunk 77 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0870
   chunk 64 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4896

-------------------------------------------------------------------------------
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 = 0.3389 r_free = 0.3389 target = 0.117712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.096497 restraints weight = 12128.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.099348 restraints weight = 6859.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.101229 restraints weight = 4724.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.102465 restraints weight = 3690.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.103116 restraints weight = 3102.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7993  Z= 0.119
  Angle     :  0.549  12.434  10961  Z= 0.271
  Chirality :  0.040   0.234   1290
  Planarity :  0.003   0.027   1330
  Dihedral  :  5.244  52.905   1200
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 19.00 %
    Favored  : 76.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.00 (0.28), residues: 976
  helix:  2.66 (0.23), residues: 467
  sheet: -0.64 (0.49), residues: 111
  loop : -1.48 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 269 
 TYR   0.016   0.001   TYR B 570 
 PHE   0.018   0.001   PHE B 322 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.004   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7979)
  covalent geometry    : angle       0.51468 (10926)
  SS BOND              : bond        0.00392 (    7)
  SS BOND              : angle       0.57196 (   14)
  hydrogen bonds       : bond        0.03204 (  418)
  hydrogen bonds       : angle       4.04357 ( 1209)
  link_BETA1-4         : bond        0.00370 (    1)
  link_BETA1-4         : angle       1.76182 (    3)
  link_NAG-ASN         : bond        0.00750 (    6)
  link_NAG-ASN         : angle       4.66868 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 69
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 MET cc_start: 0.8179 (tmm) cc_final: 0.7624 (ttt)
REVERT: A  551 LYS cc_start: 0.8572 (tttt) cc_final: 0.8172 (tmtt)
REVERT: B  325 MET cc_start: 0.7765 (tpp) cc_final: 0.7480 (tpp)
  outliers start: 33
  outliers final: 30
  residues processed: 97
  average time/residue: 0.0930
  time to fit residues: 12.5237
Evaluate side-chains
  96 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  657 LYS
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.0060
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 52 optimal weight:    0.4980
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.117578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.096454 restraints weight = 12110.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.099225 restraints weight = 6803.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.101040 restraints weight = 4725.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102337 restraints weight = 3710.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.103155 restraints weight = 3125.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7993  Z= 0.129
  Angle     :  0.546  11.854  10961  Z= 0.270
  Chirality :  0.040   0.241   1290
  Planarity :  0.003   0.027   1330
  Dihedral  :  5.162  52.852   1200
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.62 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.05 (0.28), residues: 976
  helix:  2.70 (0.23), residues: 467
  sheet: -0.61 (0.49), residues: 111
  loop : -1.46 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 269 
 TYR   0.017   0.001   TYR B 570 
 PHE   0.018   0.001   PHE B 322 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7979)
  covalent geometry    : angle       0.51379 (10926)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       0.67375 (   14)
  hydrogen bonds       : bond        0.03223 (  418)
  hydrogen bonds       : angle       4.01720 ( 1209)
  link_BETA1-4         : bond        0.00301 (    1)
  link_BETA1-4         : angle       1.62241 (    3)
  link_NAG-ASN         : bond        0.00735 (    6)
  link_NAG-ASN         : angle       4.56468 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 69
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 MET cc_start: 0.8181 (tmm) cc_final: 0.7704 (ttt)
REVERT: A  551 LYS cc_start: 0.8547 (tttt) cc_final: 0.8147 (tmtt)
REVERT: B  325 MET cc_start: 0.7828 (tpp) cc_final: 0.7501 (tpp)
  outliers start: 34
  outliers final: 31
  residues processed: 98
  average time/residue: 0.0910
  time to fit residues: 12.3896
Evaluate side-chains
  99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  598 THR
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 53 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 76 optimal weight:    0.4980
   chunk 11 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.117477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.096211 restraints weight = 12116.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.099033 restraints weight = 6849.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.100928 restraints weight = 4742.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.102132 restraints weight = 3706.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.103035 restraints weight = 3125.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7993  Z= 0.133
  Angle     :  0.552  11.548  10961  Z= 0.274
  Chirality :  0.041   0.238   1290
  Planarity :  0.003   0.041   1330
  Dihedral  :  5.151  52.581   1200
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 18.75 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.04 (0.28), residues: 976
  helix:  2.69 (0.23), residues: 467
  sheet: -0.69 (0.49), residues: 111
  loop : -1.44 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 269 
 TYR   0.017   0.001   TYR B 570 
 PHE   0.018   0.001   PHE B 601 
 TRP   0.012   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7979)
  covalent geometry    : angle       0.52084 (10926)
  SS BOND              : bond        0.00247 (    7)
  SS BOND              : angle       0.56527 (   14)
  hydrogen bonds       : bond        0.03213 (  418)
  hydrogen bonds       : angle       4.00677 ( 1209)
  link_BETA1-4         : bond        0.00334 (    1)
  link_BETA1-4         : angle       1.62259 (    3)
  link_NAG-ASN         : bond        0.00715 (    6)
  link_NAG-ASN         : angle       4.49893 (   18)

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

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

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1952 Ramachandran restraints generated.
    976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 68
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  317 MET cc_start: 0.8204 (tmm) cc_final: 0.7724 (ttt)
REVERT: A  551 LYS cc_start: 0.8573 (tttt) cc_final: 0.8223 (tttp)
REVERT: A  660 PHE cc_start: 0.8388 (m-80) cc_final: 0.8166 (m-10)
REVERT: B  325 MET cc_start: 0.7827 (tpp) cc_final: 0.7509 (tpp)
  outliers start: 33
  outliers final: 32
  residues processed: 98
  average time/residue: 0.0914
  time to fit residues: 12.3962
Evaluate side-chains
  99 residues out of total 859 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 67
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 HIS
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  316 ILE
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  638 THR
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue   87 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 VAL
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  483 HIS
Chi-restraints excluded: chain B residue  531 ILE
Chi-restraints excluded: chain B residue  571 VAL
Chi-restraints excluded: chain B residue  584 VAL
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 90 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0470
   chunk 44 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.118536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.097297 restraints weight = 12005.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.100161 restraints weight = 6795.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.102130 restraints weight = 4673.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.103384 restraints weight = 3611.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.103934 restraints weight = 3043.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7993  Z= 0.114
  Angle     :  0.537  10.973  10961  Z= 0.267
  Chirality :  0.040   0.241   1290
  Planarity :  0.003   0.027   1330
  Dihedral  :  5.106  52.769   1200
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 18.88 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.13 (0.28), residues: 976
  helix:  2.77 (0.23), residues: 467
  sheet: -0.68 (0.49), residues: 111
  loop : -1.40 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 269 
 TYR   0.016   0.001   TYR B 570 
 PHE   0.029   0.001   PHE B 601 
 TRP   0.011   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 7979)
  covalent geometry    : angle       0.50664 (10926)
  SS BOND              : bond        0.00224 (    7)
  SS BOND              : angle       0.48913 (   14)
  hydrogen bonds       : bond        0.03102 (  418)
  hydrogen bonds       : angle       3.94841 ( 1209)
  link_BETA1-4         : bond        0.00359 (    1)
  link_BETA1-4         : angle       1.63159 (    3)
  link_NAG-ASN         : bond        0.00730 (    6)
  link_NAG-ASN         : angle       4.39490 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1320.65 seconds
wall clock time: 23 minutes 36.92 seconds (1416.92 seconds total)