Starting phenix.real_space_refine
on Wed Mar  4 07:31:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xci_33121/03_2026/7xci_33121.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6463 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4189      2.51       5
     N    1079      2.21       5
     O    1241      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 6547
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4869
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4990
    Chain: "B"
      Number of atoms: 1565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1565
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.47, per 1000 atoms: 0.38
  Number of scatterers: 6547
  At special positions: 0
  Unit cell: (77.22, 99.66, 114.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1241      8.00
     N    1079      7.00
     C    4189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A 702 " - " ASN A 432 "
      " NAG A 703 " - " ASN A  53 "
      " NAG A 704 " - " ASN A  90 "
      " NAG A 705 " - " ASN A 322 "
      " NAG A 706 " - " ASN A 103 "
      " NAG B 601 " - " ASN B 343 "
      " NAG C   1 " - " ASN A 546 "
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 417.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 378 "


  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      56.5% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.598A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 92 through 102
      removed outlier: 3.847A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.531A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 172
    Processing helix  chain 'A' and resid 172 through 194
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 206 through 208
      No H-bonds generated for 'chain 'A' and resid 206 through 208'
    Processing helix  chain 'A' and resid 220 through 252
      removed outlier: 3.807A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.718A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.708A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.601A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.737A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.919A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 444
      removed outlier: 3.650A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 466
      removed outlier: 3.831A  pdb=" N   THR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.531A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   MET A 480 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LYS A 481 " --> pdb=" O   TRP A 477 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.854A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLN A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLN A 526 " --> pdb=" O   GLN A 522 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A 527 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.564A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.866A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.680A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 600
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.087A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.872A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.887A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474

    305 hydrogen bonds defined for protein.
    872 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: 0.87

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.08 -     1.24: 670
        1.24 -     1.39: 2133
        1.39 -     1.54: 3845
        1.54 -     1.69: 25
        1.69 -     1.85: 59
  Bond restraints: 6732
  Sorted by residual:
  bond pdb=" CG  PRO A 469 "
       pdb=" CD  PRO A 469 "
    ideal  model  delta    sigma   weight residual
    1.503  1.084  0.419 3.40e-02 8.65e+02 1.52e+02
  bond pdb=" CG  PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.503  1.103  0.400 3.40e-02 8.65e+02 1.39e+02
  bond pdb=" N   PRO A 469 "
       pdb=" CD  PRO A 469 "
    ideal  model  delta    sigma   weight residual
    1.473  1.549 -0.076 1.40e-02 5.10e+03 2.92e+01
  bond pdb=" N   PRO A 263 "
       pdb=" CD  PRO A 263 "
    ideal  model  delta    sigma   weight residual
    1.473  1.541 -0.068 1.40e-02 5.10e+03 2.34e+01
  bond pdb=" CB  PRO A 469 "
       pdb=" CG  PRO A 469 "
    ideal  model  delta    sigma   weight residual
    1.492  1.704 -0.212 5.00e-02 4.00e+02 1.81e+01
  ... (remaining 6727 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.17: 9124
        4.17 -     8.34: 24
        8.34 -    12.51: 1
       12.51 -    16.69: 2
       16.69 -    20.86: 2
  Bond angle restraints: 9153
  Sorted by residual:
  angle pdb=" N   PRO A 263 "
        pdb=" CD  PRO A 263 "
        pdb=" CG  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     103.20   82.34   20.86 1.50e+00 4.44e-01 1.93e+02
  angle pdb=" N   PRO A 469 "
        pdb=" CD  PRO A 469 "
        pdb=" CG  PRO A 469 "
      ideal   model   delta    sigma   weight residual
     103.20   82.45   20.75 1.50e+00 4.44e-01 1.91e+02
  angle pdb=" CA  PRO A 263 "
        pdb=" CB  PRO A 263 "
        pdb=" CG  PRO A 263 "
      ideal   model   delta    sigma   weight residual
     104.50   90.21   14.29 1.90e+00 2.77e-01 5.65e+01
  angle pdb=" CA  PRO A 469 "
        pdb=" CB  PRO A 469 "
        pdb=" CG  PRO A 469 "
      ideal   model   delta    sigma   weight residual
     104.50   91.08   13.42 1.90e+00 2.77e-01 4.99e+01
  angle pdb=" CA  PRO A 469 "
        pdb=" N   PRO A 469 "
        pdb=" CD  PRO A 469 "
      ideal   model   delta    sigma   weight residual
     112.00  102.73    9.27 1.40e+00 5.10e-01 4.38e+01
  ... (remaining 9148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 3698
       17.63 -    35.26: 299
       35.26 -    52.89: 66
       52.89 -    70.52: 9
       70.52 -    88.15: 8
  Dihedral angle restraints: 4080
    sinusoidal: 1750
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" CA  PRO B 337 "
           pdb=" C   PRO B 337 "
           pdb=" N   PHE B 338 "
           pdb=" CA  PHE B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.21   25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.79  -42.79     1      1.00e+01 1.00e-02 2.56e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.69   36.31     1      1.00e+01 1.00e-02 1.86e+01
  ... (remaining 4077 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 669
       0.038 -    0.076: 232
       0.076 -    0.114: 63
       0.114 -    0.152: 12
       0.152 -    0.190: 4
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" C1  NAG A 705 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 705 "
            pdb=" O5  NAG A 705 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.00e-01
  chirality pdb=" CA  PRO B 373 "
            pdb=" N   PRO B 373 "
            pdb=" C   PRO B 373 "
            pdb=" CB  PRO B 373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" C2  NAG C   2 "
            pdb=" C1  NAG C   2 "
            pdb=" C3  NAG C   2 "
            pdb=" N2  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.32   -0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 977 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "   -0.072 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO A 469 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "   -0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 262 "   -0.059 5.00e-02 4.00e+02   8.31e-02 1.10e+01
        pdb=" N   PRO A 263 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A 263 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 263 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 414 "   -0.037 5.00e-02 4.00e+02   5.67e-02 5.14e+00
        pdb=" N   PRO A 415 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 415 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 415 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 43
        2.58 -     3.16: 5341
        3.16 -     3.74: 9924
        3.74 -     4.32: 13728
        4.32 -     4.90: 23220
  Nonbonded interactions: 52256
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.000 2.230
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER A 607 "
            pdb=" OD1 ASP A 609 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A  77 "
            pdb=" O   GLN A 101 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OE1 GLU A 189 "
            pdb=" NH2 ARG A 192 "
     model   vdw
     2.310 3.120
  ... (remaining 52251 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             13.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.490
  Find NCS groups from input model:        0.040
  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:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
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      :  0.009   0.419   6749  Z= 0.313
  Angle     :  0.759  20.857   9191  Z= 0.447
  Chirality :  0.043   0.190    980
  Planarity :  0.006   0.102   1176
  Dihedral  : 13.674  88.150   2563
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  3.30 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.57 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.57 (0.30), residues: 788
  helix:  1.09 (0.27), residues: 387
  sheet:  1.23 (0.73), residues: 50
  loop : -0.50 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 192 
 TYR   0.018   0.001   TYR A 202 
 PHE   0.022   0.001   PHE A 504 
 TRP   0.019   0.001   TRP A 165 
 HIS   0.006   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00865 ( 6732)
  covalent geometry    : angle       0.75317 ( 9153)
  SS BOND              : bond        0.00551 (    7)
  SS BOND              : angle       1.52376 (   14)
  hydrogen bonds       : bond        0.16052 (  305)
  hydrogen bonds       : angle       6.30357 (  872)
  metal coordination   : bond        0.20318 (    2)
  link_BETA1-4         : bond        0.00183 (    1)
  link_BETA1-4         : angle       0.70087 (    3)
  link_NAG-ASN         : bond        0.00325 (    7)
  link_NAG-ASN         : angle       1.81815 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  383 MET cc_start: 0.8242 (mtp) cc_final: 0.7894 (mtp)
REVERT: B  420 ASP cc_start: 0.8031 (m-30) cc_final: 0.7576 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0706
  time to fit residues: 9.7139
Evaluate side-chains
  88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0870
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
A 394 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.177542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133557 restraints weight = 8447.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 3.29
r_work: 0.3221 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3204
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6749  Z= 0.132
  Angle     :  0.568   9.323   9191  Z= 0.291
  Chirality :  0.043   0.224    980
  Planarity :  0.005   0.056   1176
  Dihedral  :  5.987  58.892   1031
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.80 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  6.17 %
    Favored  : 93.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.67 (0.30), residues: 788
  helix:  1.17 (0.26), residues: 387
  sheet:  1.17 (0.72), residues: 50
  loop : -0.43 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 192 
 TYR   0.015   0.001   TYR A 385 
 PHE   0.029   0.001   PHE A 504 
 TRP   0.019   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6732)
  covalent geometry    : angle       0.55810 ( 9153)
  SS BOND              : bond        0.00536 (    7)
  SS BOND              : angle       1.03564 (   14)
  hydrogen bonds       : bond        0.05160 (  305)
  hydrogen bonds       : angle       4.87054 (  872)
  metal coordination   : bond        0.00873 (    2)
  link_BETA1-4         : bond        0.00264 (    1)
  link_BETA1-4         : angle       1.24157 (    3)
  link_NAG-ASN         : bond        0.00281 (    7)
  link_NAG-ASN         : angle       2.08995 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  265 HIS cc_start: 0.6028 (p90) cc_final: 0.5803 (p-80)
REVERT: A  435 GLU cc_start: 0.7280 (mp0) cc_final: 0.7042 (mp0)
REVERT: B  420 ASP cc_start: 0.8513 (m-30) cc_final: 0.8095 (m-30)
  outliers start: 5
  outliers final: 2
  residues processed: 96
  average time/residue: 0.0828
  time to fit residues: 10.8560
Evaluate side-chains
  87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.173637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114516 restraints weight = 15323.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 3.55
r_work: 0.3118 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6749  Z= 0.178
  Angle     :  0.582   9.523   9191  Z= 0.298
  Chirality :  0.044   0.240    980
  Planarity :  0.005   0.048   1176
  Dihedral  :  5.665  55.784   1031
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  8.46 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    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:  0.61 (0.30), residues: 788
  helix:  1.12 (0.26), residues: 390
  sheet:  0.56 (0.67), residues: 60
  loop : -0.38 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 192 
 TYR   0.034   0.002   TYR A 381 
 PHE   0.024   0.002   PHE A 504 
 TRP   0.019   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6732)
  covalent geometry    : angle       0.56942 ( 9153)
  SS BOND              : bond        0.00364 (    7)
  SS BOND              : angle       1.26713 (   14)
  hydrogen bonds       : bond        0.05860 (  305)
  hydrogen bonds       : angle       4.74655 (  872)
  metal coordination   : bond        0.00528 (    2)
  link_BETA1-4         : bond        0.00047 (    1)
  link_BETA1-4         : angle       1.85393 (    3)
  link_NAG-ASN         : bond        0.00426 (    7)
  link_NAG-ASN         : angle       2.30077 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  435 GLU cc_start: 0.7331 (mp0) cc_final: 0.6768 (mp0)
REVERT: B  420 ASP cc_start: 0.8628 (m-30) cc_final: 0.8323 (m-30)
REVERT: B  443 SER cc_start: 0.8881 (m) cc_final: 0.8466 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0811
  time to fit residues: 10.9345
Evaluate side-chains
  88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.2980
   chunk 52 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0770
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6338

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS
A 290 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.182037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127337 restraints weight = 10568.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.81
r_work: 0.3316 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3323
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3323 r_free = 0.3323    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3323
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6749  Z= 0.131
  Angle     :  0.557   9.514   9191  Z= 0.281
  Chirality :  0.042   0.236    980
  Planarity :  0.004   0.047   1176
  Dihedral  :  5.322  55.705   1031
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.33 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.69 (0.30), residues: 788
  helix:  1.31 (0.27), residues: 383
  sheet:  0.57 (0.68), residues: 60
  loop : -0.48 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 192 
 TYR   0.018   0.001   TYR A 381 
 PHE   0.022   0.001   PHE A 504 
 TRP   0.016   0.001   TRP A 165 
 HIS   0.005   0.001   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6732)
  covalent geometry    : angle       0.54664 ( 9153)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       1.15215 (   14)
  hydrogen bonds       : bond        0.05046 (  305)
  hydrogen bonds       : angle       4.62489 (  872)
  metal coordination   : bond        0.00264 (    2)
  link_BETA1-4         : bond        0.00249 (    1)
  link_BETA1-4         : angle       1.31165 (    3)
  link_NAG-ASN         : bond        0.00263 (    7)
  link_NAG-ASN         : angle       2.12032 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  435 GLU cc_start: 0.7432 (mp0) cc_final: 0.7094 (mp0)
REVERT: B  360 ASN cc_start: 0.7584 (m-40) cc_final: 0.7270 (m-40)
REVERT: B  420 ASP cc_start: 0.8395 (m-30) cc_final: 0.8142 (m-30)
REVERT: B  443 SER cc_start: 0.8694 (m) cc_final: 0.8324 (m)
REVERT: B  517 LEU cc_start: 0.8239 (mt) cc_final: 0.8026 (mm)
  outliers start: 8
  outliers final: 5
  residues processed: 92
  average time/residue: 0.0785
  time to fit residues: 9.9931
Evaluate side-chains
  89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.0670
   chunk 63 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.182729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126251 restraints weight = 10669.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.70
r_work: 0.3364 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6749  Z= 0.124
  Angle     :  0.546   9.541   9191  Z= 0.277
  Chirality :  0.042   0.235    980
  Planarity :  0.004   0.047   1176
  Dihedral  :  5.188  55.766   1031
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.62 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.84 (0.30), residues: 788
  helix:  1.51 (0.27), residues: 375
  sheet:  0.53 (0.67), residues: 60
  loop : -0.43 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 192 
 TYR   0.017   0.001   TYR A 381 
 PHE   0.020   0.001   PHE A 504 
 TRP   0.015   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6732)
  covalent geometry    : angle       0.53366 ( 9153)
  SS BOND              : bond        0.00478 (    7)
  SS BOND              : angle       1.72799 (   14)
  hydrogen bonds       : bond        0.04847 (  305)
  hydrogen bonds       : angle       4.56145 (  872)
  metal coordination   : bond        0.00182 (    2)
  link_BETA1-4         : bond        0.00304 (    1)
  link_BETA1-4         : angle       1.29717 (    3)
  link_NAG-ASN         : bond        0.00290 (    7)
  link_NAG-ASN         : angle       2.05250 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  435 GLU cc_start: 0.7415 (mp0) cc_final: 0.7047 (mp0)
REVERT: B  360 ASN cc_start: 0.7609 (m-40) cc_final: 0.7006 (t0)
REVERT: B  420 ASP cc_start: 0.8353 (m-30) cc_final: 0.8077 (m-30)
REVERT: B  443 SER cc_start: 0.8623 (m) cc_final: 0.8235 (m)
REVERT: B  517 LEU cc_start: 0.8251 (mt) cc_final: 0.8024 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 92
  average time/residue: 0.0779
  time to fit residues: 9.8997
Evaluate side-chains
  90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS
A 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.175534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.118314 restraints weight = 16917.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 3.60
r_work: 0.3203 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6749  Z= 0.131
  Angle     :  0.548   9.587   9191  Z= 0.278
  Chirality :  0.042   0.238    980
  Planarity :  0.004   0.048   1176
  Dihedral  :  5.072  55.569   1031
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.48 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.30), residues: 788
  helix:  1.58 (0.27), residues: 375
  sheet:  0.54 (0.67), residues: 60
  loop : -0.39 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 192 
 TYR   0.018   0.001   TYR A 381 
 PHE   0.019   0.001   PHE A 504 
 TRP   0.015   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6732)
  covalent geometry    : angle       0.53654 ( 9153)
  SS BOND              : bond        0.00521 (    7)
  SS BOND              : angle       1.31483 (   14)
  hydrogen bonds       : bond        0.04926 (  305)
  hydrogen bonds       : angle       4.51446 (  872)
  metal coordination   : bond        0.00228 (    2)
  link_BETA1-4         : bond        0.00190 (    1)
  link_BETA1-4         : angle       1.37315 (    3)
  link_NAG-ASN         : bond        0.00318 (    7)
  link_NAG-ASN         : angle       2.08691 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLU cc_start: 0.7412 (mp0) cc_final: 0.6972 (mp0)
REVERT: B  360 ASN cc_start: 0.7604 (m-40) cc_final: 0.6992 (t0)
REVERT: B  420 ASP cc_start: 0.8436 (m-30) cc_final: 0.8165 (m-30)
REVERT: B  443 SER cc_start: 0.8654 (m) cc_final: 0.8251 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 91
  average time/residue: 0.0821
  time to fit residues: 10.2005
Evaluate side-chains
  92 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 66 optimal weight:    0.4980
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0870
   overall best weight:    1.1164

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.172741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.115419 restraints weight = 10412.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.77
r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6749  Z= 0.173
  Angle     :  0.581   9.669   9191  Z= 0.296
  Chirality :  0.043   0.241    980
  Planarity :  0.005   0.051   1176
  Dihedral  :  5.188  55.299   1031
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.34 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.76 (0.30), residues: 788
  helix:  1.42 (0.27), residues: 382
  sheet:  0.56 (0.69), residues: 60
  loop : -0.50 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 192 
 TYR   0.027   0.002   TYR A 381 
 PHE   0.018   0.002   PHE A 504 
 TRP   0.016   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6732)
  covalent geometry    : angle       0.56784 ( 9153)
  SS BOND              : bond        0.00532 (    7)
  SS BOND              : angle       1.53968 (   14)
  hydrogen bonds       : bond        0.05602 (  305)
  hydrogen bonds       : angle       4.60349 (  872)
  metal coordination   : bond        0.00317 (    2)
  link_BETA1-4         : bond        0.00006 (    1)
  link_BETA1-4         : angle       1.75024 (    3)
  link_NAG-ASN         : bond        0.00375 (    7)
  link_NAG-ASN         : angle       2.22328 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  435 GLU cc_start: 0.7431 (mp0) cc_final: 0.6938 (mp0)
REVERT: B  360 ASN cc_start: 0.7568 (m-40) cc_final: 0.6980 (t0)
REVERT: B  420 ASP cc_start: 0.8521 (m-30) cc_final: 0.8254 (m-30)
REVERT: B  443 SER cc_start: 0.8800 (m) cc_final: 0.8593 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0692
  time to fit residues: 8.5651
Evaluate side-chains
  87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:    0.0070
   chunk 24 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A 265 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.173075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.114552 restraints weight = 10444.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.01
r_work: 0.3160 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3152
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3152 r_free = 0.3152    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3152
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6749  Z= 0.150
  Angle     :  0.566   9.625   9191  Z= 0.288
  Chirality :  0.043   0.238    980
  Planarity :  0.004   0.053   1176
  Dihedral  :  5.167  55.297   1031
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.34 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  0.82 (0.31), residues: 788
  helix:  1.50 (0.27), residues: 381
  sheet:  0.59 (0.69), residues: 60
  loop : -0.51 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 192 
 TYR   0.023   0.001   TYR A 381 
 PHE   0.017   0.001   PHE A 504 
 TRP   0.015   0.001   TRP A 165 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6732)
  covalent geometry    : angle       0.55353 ( 9153)
  SS BOND              : bond        0.00552 (    7)
  SS BOND              : angle       1.59240 (   14)
  hydrogen bonds       : bond        0.05324 (  305)
  hydrogen bonds       : angle       4.56438 (  872)
  metal coordination   : bond        0.00289 (    2)
  link_BETA1-4         : bond        0.00106 (    1)
  link_BETA1-4         : angle       1.50471 (    3)
  link_NAG-ASN         : bond        0.00331 (    7)
  link_NAG-ASN         : angle       2.15391 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLU cc_start: 0.7448 (mp0) cc_final: 0.6943 (mp0)
REVERT: B  360 ASN cc_start: 0.7565 (m-40) cc_final: 0.6982 (t0)
REVERT: B  420 ASP cc_start: 0.8551 (m-30) cc_final: 0.8273 (m-30)
REVERT: B  443 SER cc_start: 0.8780 (m) cc_final: 0.8359 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0668
  time to fit residues: 8.7886
Evaluate side-chains
  91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  468 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.0970
   chunk 70 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.174822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142564 restraints weight = 20162.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 5.87
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6749  Z= 0.127
  Angle     :  0.548  10.254   9191  Z= 0.277
  Chirality :  0.042   0.234    980
  Planarity :  0.004   0.053   1176
  Dihedral  :  5.050  55.412   1031
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.48 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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 (0.31), residues: 788
  helix:  1.66 (0.27), residues: 375
  sheet:  0.63 (0.68), residues: 60
  loop : -0.45 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 192 
 TYR   0.018   0.001   TYR A 202 
 PHE   0.017   0.001   PHE A 504 
 TRP   0.014   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6732)
  covalent geometry    : angle       0.53621 ( 9153)
  SS BOND              : bond        0.00561 (    7)
  SS BOND              : angle       1.50051 (   14)
  hydrogen bonds       : bond        0.04850 (  305)
  hydrogen bonds       : angle       4.48188 (  872)
  metal coordination   : bond        0.00194 (    2)
  link_BETA1-4         : bond        0.00272 (    1)
  link_BETA1-4         : angle       1.17036 (    3)
  link_NAG-ASN         : bond        0.00267 (    7)
  link_NAG-ASN         : angle       2.05464 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  435 GLU cc_start: 0.7454 (mp0) cc_final: 0.7207 (mp0)
REVERT: B  360 ASN cc_start: 0.7191 (m-40) cc_final: 0.6719 (t0)
REVERT: B  420 ASP cc_start: 0.8180 (m-30) cc_final: 0.7821 (m-30)
REVERT: B  443 SER cc_start: 0.8333 (m) cc_final: 0.8080 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 89
  average time/residue: 0.0730
  time to fit residues: 9.1732
Evaluate side-chains
  90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 55 optimal weight:    0.2980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.1980
   chunk 59 optimal weight:    0.0010
   chunk 64 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0010
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.2592

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS
A 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.119215 restraints weight = 15407.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 3.54
r_work: 0.3191 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6749  Z= 0.105
  Angle     :  0.524   9.861   9191  Z= 0.264
  Chirality :  0.041   0.234    980
  Planarity :  0.004   0.051   1176
  Dihedral  :  4.815  55.612   1031
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.63 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.11 (0.31), residues: 788
  helix:  1.75 (0.27), residues: 376
  sheet:  1.19 (0.72), residues: 50
  loop : -0.39 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 192 
 TYR   0.019   0.001   TYR A 202 
 PHE   0.017   0.001   PHE A 504 
 TRP   0.013   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6732)
  covalent geometry    : angle       0.51473 ( 9153)
  SS BOND              : bond        0.00486 (    7)
  SS BOND              : angle       1.28075 (   14)
  hydrogen bonds       : bond        0.04123 (  305)
  hydrogen bonds       : angle       4.36954 (  872)
  metal coordination   : bond        0.00095 (    2)
  link_BETA1-4         : bond        0.00365 (    1)
  link_BETA1-4         : angle       0.80156 (    3)
  link_NAG-ASN         : bond        0.00229 (    7)
  link_NAG-ASN         : angle       1.89098 (   21)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 GLU cc_start: 0.7328 (mp0) cc_final: 0.6921 (mp0)
REVERT: B  360 ASN cc_start: 0.7369 (m-40) cc_final: 0.6879 (t0)
REVERT: B  420 ASP cc_start: 0.8553 (m-30) cc_final: 0.8229 (m-30)
REVERT: B  443 SER cc_start: 0.8666 (m) cc_final: 0.8243 (m)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0772
  time to fit residues: 9.5733
Evaluate side-chains
  89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 77 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 265 HIS
A 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.174567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.116472 restraints weight = 16878.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.72
r_work: 0.3148 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6749  Z= 0.141
  Angle     :  0.552   9.887   9191  Z= 0.278
  Chirality :  0.042   0.241    980
  Planarity :  0.004   0.050   1176
  Dihedral  :  4.848  55.513   1031
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 13.63 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    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:  1.03 (0.31), residues: 788
  helix:  1.69 (0.27), residues: 376
  sheet:  0.61 (0.67), residues: 60
  loop : -0.37 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 192 
 TYR   0.023   0.001   TYR A 381 
 PHE   0.025   0.001   PHE A 400 
 TRP   0.016   0.001   TRP A 165 
 HIS   0.003   0.001   HIS A 378 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6732)
  covalent geometry    : angle       0.54112 ( 9153)
  SS BOND              : bond        0.00544 (    7)
  SS BOND              : angle       1.44708 (   14)
  hydrogen bonds       : bond        0.04883 (  305)
  hydrogen bonds       : angle       4.41517 (  872)
  metal coordination   : bond        0.00268 (    2)
  link_BETA1-4         : bond        0.00055 (    1)
  link_BETA1-4         : angle       1.33652 (    3)
  link_NAG-ASN         : bond        0.00278 (    7)
  link_NAG-ASN         : angle       2.03787 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2257.95 seconds
wall clock time: 39 minutes 10.45 seconds (2350.45 seconds total)