Starting phenix.real_space_refine
on Tue Mar  3 17:41:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gjb_51386/03_2026/9gjb_51386.map"
  }
  resolution = 3.5
  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=   0.002 sd=   0.151
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      69      5.16       5
     C    4691      2.51       5
     N    1265      2.21       5
     O    1508      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7533
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 5113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 646, 5113
          Classifications: {'peptide': 646}
          Link IDs: {'PTRANS': 17, 'TRANS': 628}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 2270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 275, 2270
          Classifications: {'peptide': 275}
          Link IDs: {'PTRANS': 16, 'TRANS': 258}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.65, per 1000 atoms: 0.22
  Number of scatterers: 7533
  At special positions: 0
  Unit cell: (98.176, 94.848, 114.816, 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      69     16.00
     O    1508      8.00
     N    1265      7.00
     C    4691      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=26, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  69 " - pdb=" SG  CYS H  78 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 104 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 139 " - pdb=" SG  CYS H 169 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 395 " - pdb=" SG  CYS H 404 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 400 " - pdb=" SG  CYS H 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 412 " - pdb=" SG  CYS H 425 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 415 " - pdb=" SG  CYS L  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 416 " - pdb=" SG  CYS H 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 420 " - pdb=" SG  CYS H 456 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 446 " - pdb=" SG  CYS H 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 450 " - pdb=" SG  CYS H 482 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 471 " - pdb=" SG  CYS H 492 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 477 " - pdb=" SG  CYS H 515 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 498 " - pdb=" SG  CYS H 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 510 " - pdb=" SG  CYS H 544 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 532 " - pdb=" SG  CYS H 550 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 539 " - pdb=" SG  CYS H 573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 557 " - pdb=" SG  CYS H 580 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 568 " - pdb=" SG  CYS H 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 586 " - pdb=" SG  CYS H 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 592 " - pdb=" SG  CYS H 630 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 601 " - pdb=" SG  CYS H 613 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 622 " - pdb=" SG  CYS H 639 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 644 " - pdb=" SG  CYS H 658 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  71 " - pdb=" SG  CYS L  74 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 241 " - pdb=" SG  CYS L 274 " 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
    ALPHA1-2
      " MAN B   4 " - " MAN B   5 "
      " MAN B   5 " - " MAN B   6 "
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   7 "
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A   1 " - " ASN H 337 "
      " NAG B   1 " - " ASN H 390 "
      " NAG H 701 " - " ASN H 468 "
      " NAG H 702 " - " ASN H 198 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 277.7 milliseconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 19 sheets defined
      15.7% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'H' and resid 29 through 34
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.994A  pdb=" N   ILE H  94 " --> pdb=" O   VAL H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 125 through 129
      removed outlier: 3.582A  pdb=" N   ARG H 128 " --> pdb=" O   ASP H 125 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE H 129 " --> pdb=" O   GLU H 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 125 through 129'
    Processing helix  chain 'H' and resid 188 through 196
      removed outlier: 3.923A  pdb=" N   ILE H 192 " --> pdb=" O   ASN H 188 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 224 through 235
      removed outlier: 4.484A  pdb=" N   LYS H 229 " --> pdb=" O   SER H 225 " (cutoff:3.500A)
      removed outlier: 5.851A  pdb=" N   SER H 230 " --> pdb=" O   THR H 226 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 236 through 241
    Processing helix  chain 'H' and resid 263 through 267
    Processing helix  chain 'H' and resid 268 through 274
      removed outlier: 3.544A  pdb=" N   LYS H 274 " --> pdb=" O   ASP H 270 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 282 through 299
      removed outlier: 3.595A  pdb=" N   ASP H 299 " --> pdb=" O   THR H 295 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 350 through 359
      removed outlier: 3.879A  pdb=" N   THR H 354 " --> pdb=" O   ASP H 350 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG H 359 " --> pdb=" O   ARG H 355 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 372 through 374
      No H-bonds generated for 'chain 'H' and resid 372 through 374'
    Processing helix  chain 'H' and resid 375 through 391
    Processing helix  chain 'H' and resid 396 through 400
      removed outlier: 3.775A  pdb=" N   CYS H 400 " --> pdb=" O   ARG H 397 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 560 through 564
    Processing helix  chain 'H' and resid 604 through 608
    Processing helix  chain 'L' and resid 92 through 98
    Processing helix  chain 'L' and resid 135 through 138
      removed outlier: 3.871A  pdb=" N   GLN L 138 " --> pdb=" O   ASN L 135 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 135 through 138'
    Processing helix  chain 'L' and resid 182 through 187
      removed outlier: 3.928A  pdb=" N   ASN L 187 " --> pdb=" O   PRO L 183 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 197 through 201
    Processing helix  chain 'L' and resid 222 through 226
    Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108
      removed outlier: 3.598A  pdb=" N   HIS H  63 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   CYS H 169 " --> pdb=" O   PHE H 181 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TYR H 152 " --> pdb=" O   CYS H 169 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   MET H 171 " --> pdb=" O   TYR H 150 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TYR H 150 " --> pdb=" O   MET H 171 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   PHE H 173 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   LEU H 148 " --> pdb=" O   PHE H 173 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108
      removed outlier: 3.598A  pdb=" N   HIS H  63 " --> pdb=" O   TYR H  55 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262
      removed outlier: 7.442A  pdb=" N   THR H 214 " --> pdb=" O   GLY H 246 " (cutoff:3.500A)
      removed outlier: 9.002A  pdb=" N   THR H 248 " --> pdb=" O   THR H 214 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LEU H 216 " --> pdb=" O   THR H 248 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   TYR H 250 " --> pdb=" O   LEU H 216 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   ILE H 218 " --> pdb=" O   TYR H 250 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   LEU H 252 " --> pdb=" O   ILE H 218 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   HIS H 215 " --> pdb=" O   THR H 314 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ILE H 316 " --> pdb=" O   HIS H 215 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   ALA H 217 " --> pdb=" O   ILE H 316 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   LEU H 318 " --> pdb=" O   ALA H 217 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE H 219 " --> pdb=" O   LEU H 318 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   GLY H 313 " --> pdb=" O   SER H 339 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   HIS H 341 " --> pdb=" O   GLY H 313 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   MET H 315 " --> pdb=" O   HIS H 341 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   VAL H 343 " --> pdb=" O   MET H 315 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL H 317 " --> pdb=" O   VAL H 343 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   LEU H 345 " --> pdb=" O   VAL H 317 " (cutoff:3.500A)
      removed outlier: 8.133A  pdb=" N   HIS H 368 " --> pdb=" O   VAL H 340 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   THR H 342 " --> pdb=" O   HIS H 368 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   PHE H 370 " --> pdb=" O   THR H 342 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   VAL H 344 " --> pdb=" O   PHE H 370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404
    Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 426
    Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456
      removed outlier: 6.870A  pdb=" N   SER H 453 " --> pdb=" O   THR H 465 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 478 through 481
    Processing sheet with id=AA8, first strand: chain 'H' and resid 512 through 515
      removed outlier: 6.142A  pdb=" N   THR H 514 " --> pdb=" O   LYS H 524 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   LYS H 524 " --> pdb=" O   THR H 514 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 544
    Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 573
    Processing sheet with id=AB2, first strand: chain 'H' and resid 628 through 630
    Processing sheet with id=AB3, first strand: chain 'H' and resid 650 through 651
    Processing sheet with id=AB4, first strand: chain 'L' and resid 77 through 81
    Processing sheet with id=AB5, first strand: chain 'L' and resid 83 through 84
    Processing sheet with id=AB6, first strand: chain 'L' and resid 103 through 107
      removed outlier: 6.669A  pdb=" N   ILE L 126 " --> pdb=" O   ILE L 269 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE L 269 " --> pdb=" O   ILE L 126 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 140 through 143
      removed outlier: 3.637A  pdb=" N   MET L 147 " --> pdb=" O   ALA L 143 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 156 through 160
    Processing sheet with id=AB9, first strand: chain 'L' and resid 191 through 193
      removed outlier: 3.811A  pdb=" N   HIS L 229 " --> pdb=" O   VAL L 193 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 207 through 212

    210 hydrogen bonds defined for protein.
    534 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: 1.40

  Time building geometry restraints manager: 0.91 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: 2415
        1.34 -     1.46: 1692
        1.46 -     1.58: 3497
        1.58 -     1.70: 0
        1.70 -     1.81: 85
  Bond restraints: 7689
  Sorted by residual:
  bond pdb=" CB  ASP H 320 "
       pdb=" CG  ASP H 320 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 8.91e-01
  bond pdb=" CB  ASP H 133 "
       pdb=" CG  ASP H 133 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 8.85e-01
  bond pdb=" CA  ASP H 320 "
       pdb=" CB  ASP H 320 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.87e-01
  bond pdb=" CB  ASN L  25 "
       pdb=" CG  ASN L  25 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.56e-01
  bond pdb=" CB  ASN L  65 "
       pdb=" CG  ASN L  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 2.50e-02 1.60e+03 6.01e-01
  ... (remaining 7684 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 10254
        1.69 -     3.39: 125
        3.39 -     5.08: 19
        5.08 -     6.77: 2
        6.77 -     8.47: 3
  Bond angle restraints: 10403
  Sorted by residual:
  angle pdb=" CA  LEU H 584 "
        pdb=" CB  LEU H 584 "
        pdb=" CG  LEU H 584 "
      ideal   model   delta    sigma   weight residual
     116.30  124.77   -8.47 3.50e+00 8.16e-02 5.85e+00
  angle pdb=" C   ASP H 469 "
        pdb=" N   THR H 470 "
        pdb=" CA  THR H 470 "
      ideal   model   delta    sigma   weight residual
     121.54  126.12   -4.58 1.91e+00 2.74e-01 5.75e+00
  angle pdb=" CA  LEU H 323 "
        pdb=" CB  LEU H 323 "
        pdb=" CG  LEU H 323 "
      ideal   model   delta    sigma   weight residual
     116.30  124.01   -7.71 3.50e+00 8.16e-02 4.85e+00
  angle pdb=" CA  ASP H 133 "
        pdb=" CB  ASP H 133 "
        pdb=" CG  ASP H 133 "
      ideal   model   delta    sigma   weight residual
     112.60  114.70   -2.10 1.00e+00 1.00e+00 4.43e+00
  angle pdb=" N   TRP L 223 "
        pdb=" CA  TRP L 223 "
        pdb=" C   TRP L 223 "
      ideal   model   delta    sigma   weight residual
     109.81  114.45   -4.64 2.21e+00 2.05e-01 4.42e+00
  ... (remaining 10398 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4134
       17.68 -    35.35: 537
       35.35 -    53.03: 148
       53.03 -    70.70: 40
       70.70 -    88.38: 22
  Dihedral angle restraints: 4881
    sinusoidal: 2153
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" CB  CYS H 557 "
           pdb=" SG  CYS H 557 "
           pdb=" SG  CYS H 580 "
           pdb=" CB  CYS H 580 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.02  -86.02     1      1.00e+01 1.00e-02 8.93e+01
  dihedral pdb=" CB  CYS H 532 "
           pdb=" SG  CYS H 532 "
           pdb=" SG  CYS H 550 "
           pdb=" CB  CYS H 550 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -2.13  -83.87     1      1.00e+01 1.00e-02 8.58e+01
  dihedral pdb=" CB  CYS H 420 "
           pdb=" SG  CYS H 420 "
           pdb=" SG  CYS H 456 "
           pdb=" CB  CYS H 456 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.32   81.32     1      1.00e+01 1.00e-02 8.15e+01
  ... (remaining 4878 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 785
       0.036 -    0.072: 266
       0.072 -    0.108: 83
       0.108 -    0.144: 24
       0.144 -    0.180: 2
  Chirality restraints: 1160
  Sorted by residual:
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN H 337 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN H 390 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.25   -0.15 2.00e-01 2.50e+01 5.50e-01
  chirality pdb=" CA  ILE L 126 "
            pdb=" N   ILE L 126 "
            pdb=" C   ILE L 126 "
            pdb=" CB  ILE L 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 1157 not shown)

  Planarity restraints: 1332
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L  39 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.67e+00
        pdb=" N   PRO L  40 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO L  40 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L  40 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP L 173 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.27e+00
        pdb=" N   PRO L 174 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO L 174 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L 174 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN L  65 "   -0.007 2.00e-02 2.50e+03   1.32e-02 1.75e+00
        pdb=" C   ASN L  65 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ASN L  65 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   TYR L  66 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1329 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1158
        2.76 -     3.30: 6735
        3.30 -     3.83: 11879
        3.83 -     4.37: 13779
        4.37 -     4.90: 24635
  Nonbonded interactions: 58186
  Sorted by model distance:
  nonbonded pdb=" O   VAL H 212 "
            pdb=" OG1 THR H 243 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   LYS L 222 "
            pdb=" OG1 THR L 225 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   TYR H 195 "
            pdb=" OG1 THR H 199 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" N   GLU H 499 "
            pdb=" OE1 GLU H 499 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   SER H 230 "
            pdb=" ND2 ASN H 234 "
     model   vdw
     2.293 3.120
  ... (remaining 58181 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.410
  Find NCS groups from input model:        0.030
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
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      :  0.002   0.024   7727  Z= 0.095
  Angle     :  0.516   8.467  10491  Z= 0.269
  Chirality :  0.042   0.180   1160
  Planarity :  0.003   0.041   1328
  Dihedral  : 17.576  88.379   3053
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 26.35 %
    Favored  : 73.53 %
  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 are not related in a simple way.
  whole: -0.53 (0.27), residues: 915
  helix:  0.06 (0.56), residues: 97
  sheet: -0.49 (0.36), residues: 219
  loop : -0.30 (0.24), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 583 
 TYR   0.015   0.001   TYR L  28 
 PHE   0.008   0.001   PHE H 258 
 TRP   0.007   0.001   TRP H  66 
 HIS   0.001   0.000   HIS H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 ( 7689)
  covalent geometry    : angle       0.50823 (10403)
  SS BOND              : bond        0.00170 (   26)
  SS BOND              : angle       0.72495 (   52)
  hydrogen bonds       : bond        0.16021 (  185)
  hydrogen bonds       : angle       6.62471 (  534)
  link_ALPHA1-2        : bond        0.00493 (    2)
  link_ALPHA1-2        : angle       1.43758 (    6)
  link_ALPHA1-3        : bond        0.00325 (    1)
  link_ALPHA1-3        : angle       1.48626 (    3)
  link_ALPHA1-6        : bond        0.00546 (    1)
  link_ALPHA1-6        : angle       1.28461 (    3)
  link_BETA1-4         : bond        0.00533 (    4)
  link_BETA1-4         : angle       1.89314 (   12)
  link_NAG-ASN         : bond        0.00263 (    4)
  link_NAG-ASN         : angle       1.18722 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: H  583 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6826 (mtp85)
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0896
  time to fit residues: 9.9017
Evaluate side-chains
  77 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  582 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    0.0170
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
H  44 HIS
H 210 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.214355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.162162 restraints weight = 6968.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.162603 restraints weight = 6342.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.163475 restraints weight = 6095.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.163737 restraints weight = 5723.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.163889 restraints weight = 5583.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   7727  Z= 0.239
  Angle     :  0.635   6.524  10491  Z= 0.329
  Chirality :  0.048   0.226   1160
  Planarity :  0.004   0.038   1328
  Dihedral  :  8.484  68.944   1260
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 23.59 %
    Favored  : 72.80 %
  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 are not related in a simple way.
  whole: -1.00 (0.26), residues: 915
  helix: -0.46 (0.51), residues: 103
  sheet: -0.84 (0.33), residues: 227
  loop : -0.57 (0.24), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 409 
 TYR   0.019   0.002   TYR H 251 
 PHE   0.023   0.002   PHE H  53 
 TRP   0.012   0.002   TRP H 435 
 HIS   0.003   0.001   HIS H  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 7689)
  covalent geometry    : angle       0.61941 (10403)
  SS BOND              : bond        0.00477 (   26)
  SS BOND              : angle       1.08470 (   52)
  hydrogen bonds       : bond        0.04152 (  185)
  hydrogen bonds       : angle       5.74505 (  534)
  link_ALPHA1-2        : bond        0.00561 (    2)
  link_ALPHA1-2        : angle       1.36957 (    6)
  link_ALPHA1-3        : bond        0.00714 (    1)
  link_ALPHA1-3        : angle       1.90677 (    3)
  link_ALPHA1-6        : bond        0.00042 (    1)
  link_ALPHA1-6        : angle       1.61957 (    3)
  link_BETA1-4         : bond        0.00435 (    4)
  link_BETA1-4         : angle       2.87135 (   12)
  link_NAG-ASN         : bond        0.00219 (    4)
  link_NAG-ASN         : angle       1.87701 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6987 (tmm)
REVERT: H  478 MET cc_start: 0.6125 (tpp) cc_final: 0.5826 (tpp)
REVERT: L   76 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7520 (mtt90)
REVERT: L  110 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7781 (t0)
  outliers start: 30
  outliers final: 14
  residues processed: 105
  average time/residue: 0.0931
  time to fit residues: 12.8314
Evaluate side-chains
  96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   89 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  464 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  552 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue   93 ASP
Chi-restraints excluded: chain L residue  105 MET
Chi-restraints excluded: chain L residue  110 ASP
Chi-restraints excluded: chain L residue  127 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0050
   chunk 90 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
H 210 ASN
** H 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 138 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.218980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.171936 restraints weight = 6927.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.171806 restraints weight = 6518.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.171781 restraints weight = 6309.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.171895 restraints weight = 5810.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.172032 restraints weight = 5681.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7727  Z= 0.107
  Angle     :  0.523   5.520  10491  Z= 0.271
  Chirality :  0.044   0.206   1160
  Planarity :  0.003   0.038   1328
  Dihedral  :  7.037  58.175   1258
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 24.19 %
    Favored  : 73.89 %
  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 are not related in a simple way.
  whole: -0.83 (0.27), residues: 915
  helix: -0.18 (0.53), residues: 102
  sheet: -0.71 (0.34), residues: 232
  loop : -0.49 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 583 
 TYR   0.013   0.001   TYR H  50 
 PHE   0.012   0.001   PHE H  53 
 TRP   0.007   0.001   TRP L 223 
 HIS   0.002   0.001   HIS H 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7689)
  covalent geometry    : angle       0.50926 (10403)
  SS BOND              : bond        0.00208 (   26)
  SS BOND              : angle       0.85324 (   52)
  hydrogen bonds       : bond        0.03324 (  185)
  hydrogen bonds       : angle       5.38251 (  534)
  link_ALPHA1-2        : bond        0.00287 (    2)
  link_ALPHA1-2        : angle       1.43541 (    6)
  link_ALPHA1-3        : bond        0.01034 (    1)
  link_ALPHA1-3        : angle       1.91793 (    3)
  link_ALPHA1-6        : bond        0.00307 (    1)
  link_ALPHA1-6        : angle       1.50210 (    3)
  link_BETA1-4         : bond        0.00547 (    4)
  link_BETA1-4         : angle       2.45909 (   12)
  link_NAG-ASN         : bond        0.00227 (    4)
  link_NAG-ASN         : angle       1.56692 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6695 (tmm)
REVERT: H  478 MET cc_start: 0.6365 (tpp) cc_final: 0.5896 (tpp)
REVERT: H  583 ARG cc_start: 0.7335 (ttm-80) cc_final: 0.6850 (mtp85)
REVERT: L   95 ASP cc_start: 0.6906 (m-30) cc_final: 0.6523 (m-30)
  outliers start: 16
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0929
  time to fit residues: 11.6434
Evaluate side-chains
  82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0060
   chunk 68 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
H 582 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.218727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.187538 restraints weight = 7002.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.187153 restraints weight = 10764.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.188359 restraints weight = 10680.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.187208 restraints weight = 7836.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.188179 restraints weight = 7445.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7727  Z= 0.104
  Angle     :  0.510   5.515  10491  Z= 0.264
  Chirality :  0.044   0.201   1160
  Planarity :  0.003   0.037   1328
  Dihedral  :  6.236  55.742   1258
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 23.71 %
    Favored  : 73.89 %
  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 are not related in a simple way.
  whole: -0.79 (0.27), residues: 915
  helix: -0.04 (0.54), residues: 102
  sheet: -0.65 (0.35), residues: 222
  loop : -0.51 (0.25), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 583 
 TYR   0.010   0.001   TYR H 467 
 PHE   0.011   0.001   PHE H  53 
 TRP   0.006   0.001   TRP L 223 
 HIS   0.002   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7689)
  covalent geometry    : angle       0.49830 (10403)
  SS BOND              : bond        0.00210 (   26)
  SS BOND              : angle       0.73829 (   52)
  hydrogen bonds       : bond        0.03035 (  185)
  hydrogen bonds       : angle       5.16754 (  534)
  link_ALPHA1-2        : bond        0.00409 (    2)
  link_ALPHA1-2        : angle       1.46655 (    6)
  link_ALPHA1-3        : bond        0.01111 (    1)
  link_ALPHA1-3        : angle       1.97647 (    3)
  link_ALPHA1-6        : bond        0.00419 (    1)
  link_ALPHA1-6        : angle       1.56307 (    3)
  link_BETA1-4         : bond        0.00544 (    4)
  link_BETA1-4         : angle       2.26079 (   12)
  link_NAG-ASN         : bond        0.00229 (    4)
  link_NAG-ASN         : angle       1.49326 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6554 (tmm)
REVERT: H  455 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8002 (tm-30)
REVERT: H  478 MET cc_start: 0.5930 (tpp) cc_final: 0.5679 (tpp)
REVERT: H  583 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.6953 (mtp85)
REVERT: L   95 ASP cc_start: 0.6922 (m-30) cc_final: 0.6601 (m-30)
  outliers start: 20
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1067
  time to fit residues: 13.0085
Evaluate side-chains
  85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  420 CYS
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:   20.0000
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 51 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   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 = 0.4314 r_free = 0.4314 target = 0.217897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.167995 restraints weight = 6942.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.168965 restraints weight = 6208.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.169568 restraints weight = 5774.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.170001 restraints weight = 5367.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.170161 restraints weight = 5343.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7727  Z= 0.117
  Angle     :  0.522   5.691  10491  Z= 0.270
  Chirality :  0.044   0.207   1160
  Planarity :  0.003   0.039   1328
  Dihedral  :  5.970  56.217   1258
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 23.71 %
    Favored  : 73.77 %
  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 are not related in a simple way.
  whole: -0.87 (0.27), residues: 915
  helix: -0.30 (0.52), residues: 108
  sheet: -0.68 (0.34), residues: 222
  loop : -0.54 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L 280 
 TYR   0.010   0.001   TYR H 251 
 PHE   0.012   0.001   PHE H  53 
 TRP   0.006   0.001   TRP H 435 
 HIS   0.002   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7689)
  covalent geometry    : angle       0.50968 (10403)
  SS BOND              : bond        0.00209 (   26)
  SS BOND              : angle       0.85545 (   52)
  hydrogen bonds       : bond        0.03101 (  185)
  hydrogen bonds       : angle       5.16091 (  534)
  link_ALPHA1-2        : bond        0.00342 (    2)
  link_ALPHA1-2        : angle       1.45018 (    6)
  link_ALPHA1-3        : bond        0.01090 (    1)
  link_ALPHA1-3        : angle       1.88612 (    3)
  link_ALPHA1-6        : bond        0.00454 (    1)
  link_ALPHA1-6        : angle       1.46098 (    3)
  link_BETA1-4         : bond        0.00504 (    4)
  link_BETA1-4         : angle       2.27140 (   12)
  link_NAG-ASN         : bond        0.00199 (    4)
  link_NAG-ASN         : angle       1.50842 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6674 (tmm)
REVERT: H  455 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7848 (tm-30)
REVERT: H  583 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6835 (mtp85)
REVERT: L   76 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7363 (mtt90)
  outliers start: 21
  outliers final: 13
  residues processed: 91
  average time/residue: 0.1026
  time to fit residues: 12.4153
Evaluate side-chains
  92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  399 LYS
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4306 r_free = 0.4306 target = 0.216879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 108)---------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.170824 restraints weight = 6952.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.168846 restraints weight = 7092.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.168631 restraints weight = 7619.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.168685 restraints weight = 8193.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.168904 restraints weight = 7242.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7727  Z= 0.128
  Angle     :  0.524   5.933  10491  Z= 0.272
  Chirality :  0.044   0.212   1160
  Planarity :  0.003   0.040   1328
  Dihedral  :  5.858  57.338   1258
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.10 %
    Favored  : 73.53 %
  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 are not related in a simple way.
  whole: -0.89 (0.27), residues: 915
  helix: -0.26 (0.52), residues: 108
  sheet: -0.74 (0.34), residues: 222
  loop : -0.54 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 280 
 TYR   0.011   0.001   TYR H 251 
 PHE   0.014   0.001   PHE H  53 
 TRP   0.008   0.001   TRP H 435 
 HIS   0.003   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7689)
  covalent geometry    : angle       0.51094 (10403)
  SS BOND              : bond        0.00222 (   26)
  SS BOND              : angle       0.93658 (   52)
  hydrogen bonds       : bond        0.03132 (  185)
  hydrogen bonds       : angle       5.15465 (  534)
  link_ALPHA1-2        : bond        0.00365 (    2)
  link_ALPHA1-2        : angle       1.46045 (    6)
  link_ALPHA1-3        : bond        0.01160 (    1)
  link_ALPHA1-3        : angle       1.96649 (    3)
  link_ALPHA1-6        : bond        0.00495 (    1)
  link_ALPHA1-6        : angle       1.43582 (    3)
  link_BETA1-4         : bond        0.00543 (    4)
  link_BETA1-4         : angle       2.23509 (   12)
  link_NAG-ASN         : bond        0.00207 (    4)
  link_NAG-ASN         : angle       1.53884 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6615 (tmm)
REVERT: H  455 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7805 (tm-30)
REVERT: H  478 MET cc_start: 0.6803 (tpp) cc_final: 0.5689 (tpp)
REVERT: H  583 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.6793 (mtp85)
REVERT: L   76 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7360 (mtt90)
REVERT: L   95 ASP cc_start: 0.7148 (m-30) cc_final: 0.6700 (m-30)
REVERT: L  245 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7569 (mtt90)
  outliers start: 28
  outliers final: 18
  residues processed: 102
  average time/residue: 0.0964
  time to fit residues: 13.2772
Evaluate side-chains
  98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  536 THR
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  105 MET
Chi-restraints excluded: chain L residue  127 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 80 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0040
   overall best weight:    1.1596

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

Flipped N/Q/H residues before XYZ refinement:
L 138 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.209970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.149677 restraints weight = 7049.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.152044 restraints weight = 5860.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.153182 restraints weight = 5160.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154857 restraints weight = 4774.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.154857 restraints weight = 4540.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7727  Z= 0.140
  Angle     :  0.541   5.984  10491  Z= 0.282
  Chirality :  0.045   0.219   1160
  Planarity :  0.004   0.041   1328
  Dihedral  :  5.846  58.239   1258
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.59 %
    Favored  : 73.29 %
  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 are not related in a simple way.
  whole: -0.96 (0.27), residues: 915
  helix: -0.33 (0.52), residues: 109
  sheet: -0.88 (0.34), residues: 222
  loop : -0.54 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 280 
 TYR   0.012   0.001   TYR H 251 
 PHE   0.015   0.001   PHE H  53 
 TRP   0.008   0.001   TRP H 435 
 HIS   0.003   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 7689)
  covalent geometry    : angle       0.52870 (10403)
  SS BOND              : bond        0.00215 (   26)
  SS BOND              : angle       0.94637 (   52)
  hydrogen bonds       : bond        0.03230 (  185)
  hydrogen bonds       : angle       5.22854 (  534)
  link_ALPHA1-2        : bond        0.00377 (    2)
  link_ALPHA1-2        : angle       1.49373 (    6)
  link_ALPHA1-3        : bond        0.01194 (    1)
  link_ALPHA1-3        : angle       2.04476 (    3)
  link_ALPHA1-6        : bond        0.00489 (    1)
  link_ALPHA1-6        : angle       1.39928 (    3)
  link_BETA1-4         : bond        0.00529 (    4)
  link_BETA1-4         : angle       2.21141 (   12)
  link_NAG-ASN         : bond        0.00200 (    4)
  link_NAG-ASN         : angle       1.60083 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  159 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7199 (t80)
REVERT: H  407 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6665 (tmm)
REVERT: H  455 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7640 (tm-30)
REVERT: H  478 MET cc_start: 0.6889 (tpp) cc_final: 0.5714 (tpp)
REVERT: H  531 MET cc_start: 0.6355 (mmm) cc_final: 0.6114 (mmm)
REVERT: H  551 SER cc_start: 0.7952 (p) cc_final: 0.7621 (m)
REVERT: L   76 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7445 (mtt90)
REVERT: L   95 ASP cc_start: 0.7354 (m-30) cc_final: 0.6974 (m-30)
REVERT: L  102 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6674 (mtp180)
  outliers start: 26
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0942
  time to fit residues: 12.6816
Evaluate side-chains
  98 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  159 TYR
Chi-restraints excluded: chain H residue  207 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  219 ILE
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  321 THR
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  359 ARG
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  536 THR
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue  102 ARG
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  105 MET
Chi-restraints excluded: chain L residue  127 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 83 optimal weight:   30.0000
   chunk 57 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
L 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.211181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.150997 restraints weight = 7025.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.153593 restraints weight = 5761.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154937 restraints weight = 5075.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154937 restraints weight = 4675.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.154937 restraints weight = 4675.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7727  Z= 0.112
  Angle     :  0.517   5.684  10491  Z= 0.269
  Chirality :  0.044   0.212   1160
  Planarity :  0.003   0.041   1328
  Dihedral  :  5.577  56.155   1258
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.71 %
    Favored  : 73.53 %
  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 are not related in a simple way.
  whole: -0.89 (0.27), residues: 915
  helix: -0.26 (0.52), residues: 109
  sheet: -0.82 (0.34), residues: 222
  loop : -0.50 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 280 
 TYR   0.011   0.001   TYR L  83 
 PHE   0.012   0.001   PHE H  53 
 TRP   0.006   0.001   TRP L 223 
 HIS   0.002   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7689)
  covalent geometry    : angle       0.50548 (10403)
  SS BOND              : bond        0.00200 (   26)
  SS BOND              : angle       0.79929 (   52)
  hydrogen bonds       : bond        0.02988 (  185)
  hydrogen bonds       : angle       5.10471 (  534)
  link_ALPHA1-2        : bond        0.00317 (    2)
  link_ALPHA1-2        : angle       1.48248 (    6)
  link_ALPHA1-3        : bond        0.01183 (    1)
  link_ALPHA1-3        : angle       1.86643 (    3)
  link_ALPHA1-6        : bond        0.00606 (    1)
  link_ALPHA1-6        : angle       1.36338 (    3)
  link_BETA1-4         : bond        0.00540 (    4)
  link_BETA1-4         : angle       2.14596 (   12)
  link_NAG-ASN         : bond        0.00229 (    4)
  link_NAG-ASN         : angle       1.52576 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  159 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7196 (t80)
REVERT: H  407 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6546 (tmm)
REVERT: H  455 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7625 (tm-30)
REVERT: H  478 MET cc_start: 0.6813 (tpp) cc_final: 0.5644 (tpp)
REVERT: H  495 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7155 (ttpp)
REVERT: H  551 SER cc_start: 0.7969 (p) cc_final: 0.7607 (m)
REVERT: H  583 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6637 (mtp85)
REVERT: L   76 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7423 (mtt90)
REVERT: L   95 ASP cc_start: 0.7457 (m-30) cc_final: 0.7085 (m-30)
REVERT: L  102 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6684 (mtp180)
  outliers start: 23
  outliers final: 18
  residues processed: 95
  average time/residue: 0.0982
  time to fit residues: 12.5204
Evaluate side-chains
  96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  159 TYR
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  359 ARG
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  463 VAL
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  536 THR
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue  102 ARG
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  105 MET
Chi-restraints excluded: chain L residue  127 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.212579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.153351 restraints weight = 6964.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.155730 restraints weight = 5903.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.156982 restraints weight = 5186.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.157632 restraints weight = 4741.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.158200 restraints weight = 4577.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7727  Z= 0.125
  Angle     :  0.527   5.822  10491  Z= 0.274
  Chirality :  0.044   0.212   1160
  Planarity :  0.003   0.042   1328
  Dihedral  :  5.593  56.834   1258
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.71 %
    Favored  : 73.53 %
  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 are not related in a simple way.
  whole: -0.92 (0.27), residues: 915
  helix: -0.26 (0.52), residues: 109
  sheet: -0.86 (0.34), residues: 222
  loop : -0.52 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 280 
 TYR   0.012   0.001   TYR L  28 
 PHE   0.013   0.001   PHE H  53 
 TRP   0.007   0.001   TRP H 435 
 HIS   0.002   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7689)
  covalent geometry    : angle       0.51592 (10403)
  SS BOND              : bond        0.00223 (   26)
  SS BOND              : angle       0.77986 (   52)
  hydrogen bonds       : bond        0.03059 (  185)
  hydrogen bonds       : angle       5.10701 (  534)
  link_ALPHA1-2        : bond        0.00330 (    2)
  link_ALPHA1-2        : angle       1.48466 (    6)
  link_ALPHA1-3        : bond        0.01065 (    1)
  link_ALPHA1-3        : angle       1.89993 (    3)
  link_ALPHA1-6        : bond        0.00545 (    1)
  link_ALPHA1-6        : angle       1.37563 (    3)
  link_BETA1-4         : bond        0.00537 (    4)
  link_BETA1-4         : angle       2.12116 (   12)
  link_NAG-ASN         : bond        0.00207 (    4)
  link_NAG-ASN         : angle       1.53652 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  159 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7185 (t80)
REVERT: H  407 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6578 (tmm)
REVERT: H  455 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7686 (tm-30)
REVERT: H  478 MET cc_start: 0.6783 (tpp) cc_final: 0.5580 (tpp)
REVERT: H  495 LYS cc_start: 0.7657 (ttmt) cc_final: 0.7129 (ttpp)
REVERT: H  531 MET cc_start: 0.6402 (mmm) cc_final: 0.6201 (mmm)
REVERT: L   76 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7413 (mtt90)
REVERT: L   95 ASP cc_start: 0.7442 (m-30) cc_final: 0.7079 (m-30)
REVERT: L  102 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6666 (mtp180)
  outliers start: 23
  outliers final: 16
  residues processed: 97
  average time/residue: 0.0984
  time to fit residues: 12.9321
Evaluate side-chains
  95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  159 TYR
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  359 ARG
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  536 THR
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue   76 ARG
Chi-restraints excluded: chain L residue  102 ARG
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain L residue  105 MET
Chi-restraints excluded: chain L residue  127 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0010
   chunk 57 optimal weight:   20.0000
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0570
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    0.3980
   overall best weight:    0.4908

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

Flipped N/Q/H residues before XYZ refinement:
L 138 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.214904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.155755 restraints weight = 7005.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.158302 restraints weight = 5848.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.159557 restraints weight = 5193.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.160383 restraints weight = 4801.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.160504 restraints weight = 4564.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7727  Z= 0.096
  Angle     :  0.511   6.626  10491  Z= 0.265
  Chirality :  0.043   0.205   1160
  Planarity :  0.003   0.041   1328
  Dihedral  :  5.277  53.997   1258
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 24.79 %
    Favored  : 73.16 %
  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 are not related in a simple way.
  whole: -0.75 (0.27), residues: 915
  helix: -0.18 (0.53), residues: 109
  sheet: -0.50 (0.36), residues: 210
  loop : -0.52 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L 280 
 TYR   0.012   0.001   TYR L  83 
 PHE   0.010   0.001   PHE H 258 
 TRP   0.007   0.001   TRP H  66 
 HIS   0.002   0.001   HIS H  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7689)
  covalent geometry    : angle       0.49926 (10403)
  SS BOND              : bond        0.00170 (   26)
  SS BOND              : angle       0.93268 (   52)
  hydrogen bonds       : bond        0.02814 (  185)
  hydrogen bonds       : angle       4.98554 (  534)
  link_ALPHA1-2        : bond        0.00318 (    2)
  link_ALPHA1-2        : angle       1.48566 (    6)
  link_ALPHA1-3        : bond        0.01157 (    1)
  link_ALPHA1-3        : angle       1.65635 (    3)
  link_ALPHA1-6        : bond        0.00710 (    1)
  link_ALPHA1-6        : angle       1.30979 (    3)
  link_BETA1-4         : bond        0.00543 (    4)
  link_BETA1-4         : angle       2.05542 (   12)
  link_NAG-ASN         : bond        0.00258 (    4)
  link_NAG-ASN         : angle       1.44171 (   12)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  407 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6554 (tmm)
REVERT: H  455 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7705 (tm-30)
REVERT: H  478 MET cc_start: 0.6724 (tpp) cc_final: 0.5521 (tpp)
REVERT: H  495 LYS cc_start: 0.7739 (ttmt) cc_final: 0.7197 (ttpp)
REVERT: H  531 MET cc_start: 0.6246 (mmm) cc_final: 0.5898 (mmm)
REVERT: H  583 ARG cc_start: 0.7186 (ttm-80) cc_final: 0.6692 (mtp85)
REVERT: L   95 ASP cc_start: 0.7414 (m-30) cc_final: 0.7060 (m-30)
REVERT: L  102 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6685 (mtp180)
  outliers start: 17
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1125
  time to fit residues: 12.9601
Evaluate side-chains
  89 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue  214 THR
Chi-restraints excluded: chain H residue  259 THR
Chi-restraints excluded: chain H residue  282 VAL
Chi-restraints excluded: chain H residue  343 VAL
Chi-restraints excluded: chain H residue  359 ARG
Chi-restraints excluded: chain H residue  407 MET
Chi-restraints excluded: chain H residue  423 THR
Chi-restraints excluded: chain H residue  455 GLU
Chi-restraints excluded: chain H residue  477 CYS
Chi-restraints excluded: chain H residue  558 VAL
Chi-restraints excluded: chain H residue  577 THR
Chi-restraints excluded: chain L residue   31 MET
Chi-restraints excluded: chain L residue   58 VAL
Chi-restraints excluded: chain L residue   67 VAL
Chi-restraints excluded: chain L residue  102 ARG
Chi-restraints excluded: chain L residue  105 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:   30.0000
   chunk 24 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4215 r_free = 0.4215 target = 0.210771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.150232 restraints weight = 7004.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.152818 restraints weight = 5820.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.154075 restraints weight = 5181.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.154075 restraints weight = 4768.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.154075 restraints weight = 4768.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7727  Z= 0.138
  Angle     :  0.545   6.473  10491  Z= 0.282
  Chirality :  0.044   0.211   1160
  Planarity :  0.004   0.041   1328
  Dihedral  :  5.506  56.698   1258
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 24.43 %
    Favored  : 73.04 %
  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 are not related in a simple way.
  whole: -0.85 (0.27), residues: 915
  helix: -0.24 (0.52), residues: 109
  sheet: -0.61 (0.36), residues: 210
  loop : -0.57 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 583 
 TYR   0.012   0.001   TYR L  28 
 PHE   0.015   0.001   PHE H  53 
 TRP   0.010   0.001   TRP H 435 
 HIS   0.003   0.001   HIS H  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7689)
  covalent geometry    : angle       0.53342 (10403)
  SS BOND              : bond        0.00214 (   26)
  SS BOND              : angle       0.93942 (   52)
  hydrogen bonds       : bond        0.03101 (  185)
  hydrogen bonds       : angle       5.09079 (  534)
  link_ALPHA1-2        : bond        0.00319 (    2)
  link_ALPHA1-2        : angle       1.47428 (    6)
  link_ALPHA1-3        : bond        0.01027 (    1)
  link_ALPHA1-3        : angle       1.85620 (    3)
  link_ALPHA1-6        : bond        0.00514 (    1)
  link_ALPHA1-6        : angle       1.37185 (    3)
  link_BETA1-4         : bond        0.00534 (    4)
  link_BETA1-4         : angle       2.09180 (   12)
  link_NAG-ASN         : bond        0.00181 (    4)
  link_NAG-ASN         : angle       1.51802 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1395.56 seconds
wall clock time: 24 minutes 49.14 seconds (1489.14 seconds total)