Starting phenix.real_space_refine
on Tue Feb 11 19:48:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wgw_37517/02_2025/8wgw_37517.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.005 sd=   0.079
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4199      2.51       5
     N    1084      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6564
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1589
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 198, 1578
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
      Conformer: "B"
        Number of residues, atoms: 198, 1578
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          bond proxies already assigned to first conformer: 1613
    Chain: "B"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    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: 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
    Chain: "B"
      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
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 493 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 493 " occ=0.50
  Time building chain proxies: 5.68, per 1000 atoms: 0.87
  Number of scatterers: 6564
  At special positions: 0
  Unit cell: (82.016, 84.812, 119.296, 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    1243      8.00
     N    1084      7.00
     C    4199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 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 A1301 " - " ASN A 343 "
      " NAG B 701 " - " ASN B 322 "
      " NAG B 702 " - " ASN B 432 "
      " NAG B 703 " - " ASN B 103 "
      " NAG B 704 " - " ASN B  90 "
      " NAG B 705 " - " ASN B  53 "
      " NAG C   1 " - " ASN B 546 "
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      51.6% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.588A  pdb=" N   LEU A 368 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.436A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'B' and resid 20 through 53
      removed outlier: 3.690A  pdb=" N   HIS B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 81
      removed outlier: 3.613A  pdb=" N   GLN B  60 " --> pdb=" O   GLU B  56 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 101
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.533A  pdb=" N   SER B 106 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL B 107 " --> pdb=" O   GLY B 104 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU B 108 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 103 through 108'
    Processing helix  chain 'B' and resid 109 through 129
    Processing helix  chain 'B' and resid 145 through 155
      removed outlier: 3.670A  pdb=" N   ASN B 149 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ILE B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   MET B 152 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 172
    Processing helix  chain 'B' and resid 173 through 175
      No H-bonds generated for 'chain 'B' and resid 173 through 175'
    Processing helix  chain 'B' and resid 176 through 194
      removed outlier: 3.602A  pdb=" N   VAL B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 220 through 227
      removed outlier: 3.709A  pdb=" N   GLU B 224 " --> pdb=" O   GLY B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 247
    Processing helix  chain 'B' and resid 293 through 300
    Processing helix  chain 'B' and resid 303 through 319
    Processing helix  chain 'B' and resid 324 through 331
      removed outlier: 3.777A  pdb=" N   TRP B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU B 329 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 386
    Processing helix  chain 'B' and resid 399 through 413
      removed outlier: 3.654A  pdb=" N   ALA B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET B 408 " --> pdb=" O   VAL B 404 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER B 409 " --> pdb=" O   GLY B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 422
      removed outlier: 3.702A  pdb=" N   SER B 420 " --> pdb=" O   LYS B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 444
      removed outlier: 3.968A  pdb=" N   GLU B 435 " --> pdb=" O   ASP B 431 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE B 436 " --> pdb=" O   ASN B 432 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASN B 437 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 466
    Processing helix  chain 'B' and resid 469 through 471
      No H-bonds generated for 'chain 'B' and resid 469 through 471'
    Processing helix  chain 'B' and resid 472 through 482
    Processing helix  chain 'B' and resid 498 through 502
    Processing helix  chain 'B' and resid 505 through 509
      removed outlier: 4.084A  pdb=" N   ASP B 509 " --> pdb=" O   VAL B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 532
      removed outlier: 4.258A  pdb=" N   TYR B 516 " --> pdb=" O   PHE B 512 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE B 523 " --> pdb=" O   THR B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 542
      removed outlier: 3.584A  pdb=" N   LYS B 541 " --> pdb=" O   PRO B 538 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   CYS B 542 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 538 through 542'
    Processing helix  chain 'B' and resid 547 through 559
      removed outlier: 3.794A  pdb=" N   MET B 557 " --> pdb=" O   LYS B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 572
    Processing helix  chain 'B' and resid 581 through 588
    Processing helix  chain 'B' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 454
      removed outlier: 5.757A  pdb=" N   TYR A 449 " --> pdb=" O   PHE A 497 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   PHE A 497 " --> pdb=" O   TYR A 449 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   TYR A 451 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'B' and resid 131 through 132
      removed outlier: 3.820A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 132 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 263
      removed outlier: 5.928A  pdb=" N   LEU B 262 " --> pdb=" O   VAL B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 352
      removed outlier: 6.052A  pdb=" N   ASP B 355 " --> pdb=" O   LEU B 351 " (cutoff:3.500A)

    289 hydrogen bonds defined for protein.
    831 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: 1.70

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2091
        1.34 -     1.46: 1586
        1.46 -     1.58: 3012
        1.58 -     1.69: 1
        1.69 -     1.81: 58
  Bond restraints: 6748
  Sorted by residual:
  bond pdb=" CB  PRO B 289 "
       pdb=" CG  PRO B 289 "
    ideal  model  delta    sigma   weight residual
    1.492  1.655 -0.163 5.00e-02 4.00e+02 1.06e+01
  bond pdb=" C1  NAG B 704 "
       pdb=" O5  NAG B 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  bond pdb=" C1  NAG B 703 "
       pdb=" O5  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.70e+00
  bond pdb=" CA  VAL B 339 "
       pdb=" CB  VAL B 339 "
    ideal  model  delta    sigma   weight residual
    1.532  1.546 -0.014 1.08e-02 8.57e+03 1.60e+00
  bond pdb=" C2  NAG B 703 "
       pdb=" N2  NAG B 703 "
    ideal  model  delta    sigma   weight residual
    1.439  1.464 -0.025 2.00e-02 2.50e+03 1.52e+00
  ... (remaining 6743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 9068
        2.39 -     4.78: 91
        4.78 -     7.16: 8
        7.16 -     9.55: 2
        9.55 -    11.94: 2
  Bond angle restraints: 9171
  Sorted by residual:
  angle pdb=" CA  PRO B 289 "
        pdb=" N   PRO B 289 "
        pdb=" CD  PRO B 289 "
      ideal   model   delta    sigma   weight residual
     112.00  100.06   11.94 1.40e+00 5.10e-01 7.27e+01
  angle pdb=" N   PRO B 289 "
        pdb=" CD  PRO B 289 "
        pdb=" CG  PRO B 289 "
      ideal   model   delta    sigma   weight residual
     103.20   96.94    6.26 1.50e+00 4.44e-01 1.74e+01
  angle pdb=" N   VAL A 367 "
        pdb=" CA  VAL A 367 "
        pdb=" C   VAL A 367 "
      ideal   model   delta    sigma   weight residual
     112.29  108.65    3.64 9.40e-01 1.13e+00 1.50e+01
  angle pdb=" N   GLY B 466 "
        pdb=" CA  GLY B 466 "
        pdb=" C   GLY B 466 "
      ideal   model   delta    sigma   weight residual
     113.18  120.66   -7.48 2.37e+00 1.78e-01 9.96e+00
  angle pdb=" N   PRO B 289 "
        pdb=" CA  PRO B 289 "
        pdb=" C   PRO B 289 "
      ideal   model   delta    sigma   weight residual
     111.03  115.70   -4.67 1.78e+00 3.16e-01 6.87e+00
  ... (remaining 9166 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.43: 3683
       21.43 -    42.85: 286
       42.85 -    64.28: 52
       64.28 -    85.70: 9
       85.70 -   107.13: 42
  Dihedral angle restraints: 4072
    sinusoidal: 1737
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CA  ASN B 338 "
           pdb=" C   ASN B 338 "
           pdb=" N   VAL B 339 "
           pdb=" CA  VAL B 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.50   21.50     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" C2  NAG B 701 "
           pdb=" C3  NAG B 701 "
           pdb=" C4  NAG B 701 "
           pdb=" O4  NAG B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   67.98  107.13     1      3.00e+01 1.11e-03 1.38e+01
  dihedral pdb=" C2  NAG B 701 "
           pdb=" C3  NAG B 701 "
           pdb=" C4  NAG B 701 "
           pdb=" C5  NAG B 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -53.19  106.97     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 4069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 726
       0.045 -    0.090: 195
       0.090 -    0.135: 55
       0.135 -    0.180: 2
       0.180 -    0.225: 2
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" CG  LEU B 267 "
            pdb=" CB  LEU B 267 "
            pdb=" CD1 LEU B 267 "
            pdb=" CD2 LEU B 267 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" C1  NAG B 702 "
            pdb=" ND2 ASN B 432 "
            pdb=" C2  NAG B 702 "
            pdb=" O5  NAG B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" C2  NAG B 703 "
            pdb=" C1  NAG B 703 "
            pdb=" C3  NAG B 703 "
            pdb=" N2  NAG B 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.31   -0.18 2.00e-01 2.50e+01 7.85e-01
  ... (remaining 977 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 288 "   -0.050 5.00e-02 4.00e+02   6.99e-02 7.82e+00
        pdb=" N   PRO B 289 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 289 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 289 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 425 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.32e+00
        pdb=" N   PRO B 426 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 478 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A 479 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 204
        2.71 -     3.26: 6682
        3.26 -     3.81: 10938
        3.81 -     4.35: 13988
        4.35 -     4.90: 23629
  Nonbonded interactions: 55441
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" OE2 GLU B 166 "
            pdb=" OG  SER B 170 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   SER A 359 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   ILE B 358 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OD1 ASP B 382 "
            pdb=" OH  TYR B 385 "
     model   vdw
     2.256 3.040
  ... (remaining 55436 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=0.50 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:             4.210
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.020
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:13.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.163   6748  Z= 0.244
  Angle     :  0.592  11.938   9171  Z= 0.303
  Chirality :  0.044   0.225    980
  Planarity :  0.005   0.070   1179
  Dihedral  : 19.741 107.128   2571
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.30), residues: 793
  helix:  0.73 (0.27), residues: 372
  sheet: -0.07 (0.73), residues: 57
  loop : -0.96 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 566 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 369 
 TYR   0.022   0.001   TYR B 381 
 ARG   0.002   0.000   ARG A 357 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  444 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7801 (mtpm)
REVERT: B   98 GLN cc_start: 0.7706 (tt0) cc_final: 0.7471 (tt0)
REVERT: B  227 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: B  383 MET cc_start: 0.9016 (mtp) cc_final: 0.8801 (mtp)
REVERT: B  597 ASP cc_start: 0.7476 (m-30) cc_final: 0.7135 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 1.2437
  time to fit residues: 155.4887
Evaluate side-chains
  90 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B  60 GLN
B 578 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.112614 restraints weight = 17731.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 3.26
r_work: 0.3131 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   6748  Z= 0.334
  Angle     :  0.669   9.458   9171  Z= 0.325
  Chirality :  0.048   0.252    980
  Planarity :  0.005   0.050   1179
  Dihedral  : 14.876  85.151   1034
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 11.19 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.30), residues: 793
  helix:  0.67 (0.27), residues: 383
  sheet: -0.12 (0.74), residues: 57
  loop : -1.04 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B 374 
 PHE   0.016   0.002   PHE B 400 
 TYR   0.039   0.002   TYR B 381 
 ARG   0.003   0.000   ARG B 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8894 (m-30) cc_final: 0.8419 (m-30)
REVERT: A  444 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7674 (mtpm)
REVERT: B   98 GLN cc_start: 0.7682 (tt0) cc_final: 0.7424 (tt0)
REVERT: B  227 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: B  383 MET cc_start: 0.8768 (mtp) cc_final: 0.8478 (mtp)
REVERT: B  479 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7502 (mt-10)
REVERT: B  571 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8107 (tt0)
REVERT: B  597 ASP cc_start: 0.7547 (m-30) cc_final: 0.7034 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 104
  average time/residue: 1.1389
  time to fit residues: 125.2485
Evaluate side-chains
  99 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  571 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0010
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN
B 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.151588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.115426 restraints weight = 14473.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.95
r_work: 0.3169 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3203
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3203 r_free = 0.3203    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3203
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6748  Z= 0.217
  Angle     :  0.599   9.634   9171  Z= 0.290
  Chirality :  0.044   0.249    980
  Planarity :  0.004   0.051   1179
  Dihedral  :  9.969  75.936   1034
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.91 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.30), residues: 793
  helix:  0.79 (0.27), residues: 377
  sheet: -0.23 (0.73), residues: 57
  loop : -0.98 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.008   0.001   HIS B  34 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.026   0.002   TYR B 381 
 ARG   0.003   0.000   ARG A 357 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.8454 (ttt180) cc_final: 0.8183 (ttt-90)
REVERT: A  420 ASP cc_start: 0.8837 (m-30) cc_final: 0.8389 (m-30)
REVERT: A  444 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7657 (mtpm)
REVERT: B   63 ASN cc_start: 0.8046 (m110) cc_final: 0.7702 (m110)
REVERT: B   98 GLN cc_start: 0.7680 (tt0) cc_final: 0.7430 (tt0)
REVERT: B  227 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  383 MET cc_start: 0.8688 (mtp) cc_final: 0.8465 (mtp)
REVERT: B  479 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: B  597 ASP cc_start: 0.7462 (m-30) cc_final: 0.6967 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 105
  average time/residue: 1.1208
  time to fit residues: 124.8160
Evaluate side-chains
  100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN
A 506 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.152072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.116288 restraints weight = 21335.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 3.53
r_work: 0.3147 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6748  Z= 0.241
  Angle     :  0.594   9.691   9171  Z= 0.288
  Chirality :  0.044   0.257    980
  Planarity :  0.004   0.055   1179
  Dihedral  :  9.100  71.849   1034
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.20 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.30), residues: 793
  helix:  0.76 (0.27), residues: 381
  sheet: -0.21 (0.73), residues: 57
  loop : -0.98 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 
 PHE   0.010   0.001   PHE B 369 
 TYR   0.024   0.002   TYR B 385 
 ARG   0.002   0.000   ARG B 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  354 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7571 (t0)
REVERT: A  420 ASP cc_start: 0.8875 (m-30) cc_final: 0.8418 (m-30)
REVERT: A  440 LYS cc_start: 0.8434 (mptt) cc_final: 0.8229 (mptm)
REVERT: A  444 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7664 (mtpm)
REVERT: B   63 ASN cc_start: 0.8045 (m110) cc_final: 0.7727 (m110)
REVERT: B   98 GLN cc_start: 0.7699 (tt0) cc_final: 0.7449 (tt0)
REVERT: B  227 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7899 (mt-10)
REVERT: B  383 MET cc_start: 0.8772 (mtp) cc_final: 0.8546 (mtp)
REVERT: B  597 ASP cc_start: 0.7470 (m-30) cc_final: 0.6944 (t0)
  outliers start: 24
  outliers final: 12
  residues processed: 106
  average time/residue: 0.9797
  time to fit residues: 110.7444
Evaluate side-chains
  100 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.151336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.114669 restraints weight = 24110.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.98
r_work: 0.3129 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3102
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3102 r_free = 0.3102    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3102
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6748  Z= 0.218
  Angle     :  0.577   9.683   9171  Z= 0.283
  Chirality :  0.043   0.263    980
  Planarity :  0.004   0.056   1179
  Dihedral  :  8.360  65.179   1034
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.21 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.30), residues: 793
  helix:  0.79 (0.27), residues: 381
  sheet: -0.27 (0.72), residues: 57
  loop : -0.95 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 
 PHE   0.011   0.001   PHE B 327 
 TYR   0.022   0.001   TYR B 385 
 ARG   0.002   0.000   ARG B 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8888 (m-30) cc_final: 0.8436 (m-30)
REVERT: A  440 LYS cc_start: 0.8472 (mptt) cc_final: 0.8245 (mptm)
REVERT: A  444 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7670 (mtpm)
REVERT: B   63 ASN cc_start: 0.8097 (m110) cc_final: 0.7728 (m110)
REVERT: B   98 GLN cc_start: 0.7718 (tt0) cc_final: 0.7468 (tt0)
REVERT: B  227 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: B  597 ASP cc_start: 0.7494 (m-30) cc_final: 0.6955 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 110
  average time/residue: 1.1017
  time to fit residues: 128.5012
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.150344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113785 restraints weight = 17252.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.16
r_work: 0.3142 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3137
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6748  Z= 0.272
  Angle     :  0.607   9.679   9171  Z= 0.296
  Chirality :  0.044   0.261    980
  Planarity :  0.004   0.060   1179
  Dihedral  :  8.140  62.380   1034
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 15.21 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.31), residues: 793
  helix:  0.76 (0.27), residues: 381
  sheet: -0.32 (0.72), residues: 57
  loop : -0.94 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.007   0.001   HIS B  34 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.021   0.002   TYR B 385 
 ARG   0.009   0.001   ARG A 357 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8873 (m-30) cc_final: 0.8398 (m-30)
REVERT: A  444 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7729 (mtpm)
REVERT: B   63 ASN cc_start: 0.8103 (m110) cc_final: 0.7725 (m110)
REVERT: B   98 GLN cc_start: 0.7703 (tt0) cc_final: 0.7480 (tt0)
REVERT: B  227 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7879 (mt-10)
REVERT: B  383 MET cc_start: 0.8961 (mtp) cc_final: 0.8715 (mtp)
REVERT: B  597 ASP cc_start: 0.7480 (m-30) cc_final: 0.6943 (t0)
  outliers start: 25
  outliers final: 14
  residues processed: 108
  average time/residue: 1.0359
  time to fit residues: 118.8686
Evaluate side-chains
  102 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.151309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115148 restraints weight = 14656.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.99
r_work: 0.3161 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6748  Z= 0.220
  Angle     :  0.581   9.675   9171  Z= 0.285
  Chirality :  0.043   0.250    980
  Planarity :  0.004   0.062   1179
  Dihedral  :  7.718  57.460   1034
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.36 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.31), residues: 793
  helix:  0.81 (0.27), residues: 380
  sheet: -0.32 (0.72), residues: 57
  loop : -0.90 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.020   0.001   TYR B 385 
 ARG   0.007   0.001   ARG A 357 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8837 (m-30) cc_final: 0.8544 (m-30)
REVERT: A  444 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7713 (mtpm)
REVERT: B   37 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6779 (mm-30)
REVERT: B   63 ASN cc_start: 0.8115 (m110) cc_final: 0.7743 (m110)
REVERT: B   98 GLN cc_start: 0.7679 (tt0) cc_final: 0.7458 (tt0)
REVERT: B  227 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: B  597 ASP cc_start: 0.7472 (m-30) cc_final: 0.6943 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 107
  average time/residue: 1.0351
  time to fit residues: 117.7972
Evaluate side-chains
  105 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   37 GLU
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 68 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 77 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.152728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.115286 restraints weight = 18207.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.39
r_work: 0.3138 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3101
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3101 r_free = 0.3101    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3101
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6748  Z= 0.215
  Angle     :  0.589   9.658   9171  Z= 0.287
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.064   1179
  Dihedral  :  7.355  57.438   1034
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.36 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.31), residues: 793
  helix:  0.82 (0.27), residues: 381
  sheet: -0.31 (0.73), residues: 57
  loop : -0.92 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 315 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.006   0.000   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8860 (m-30) cc_final: 0.8551 (m-30)
REVERT: A  444 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7754 (mtpm)
REVERT: B   63 ASN cc_start: 0.8104 (m110) cc_final: 0.7737 (m110)
REVERT: B   98 GLN cc_start: 0.7655 (tt0) cc_final: 0.7447 (tt0)
REVERT: B  227 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7908 (mt-10)
REVERT: B  597 ASP cc_start: 0.7422 (m-30) cc_final: 0.6903 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 105
  average time/residue: 1.0532
  time to fit residues: 117.4196
Evaluate side-chains
  104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  213 ASP
Chi-restraints excluded: chain B residue  257 SER
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.115349 restraints weight = 18153.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 3.37
r_work: 0.3139 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6748  Z= 0.215
  Angle     :  0.579   9.650   9171  Z= 0.284
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.065   1179
  Dihedral  :  7.121  57.430   1034
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.79 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.31), residues: 793
  helix:  0.83 (0.27), residues: 386
  sheet: -0.32 (0.72), residues: 57
  loop : -0.90 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.010   0.001   PHE B 327 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.006   0.000   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8854 (m-30) cc_final: 0.8547 (m-30)
REVERT: A  444 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7759 (mtpm)
REVERT: B   63 ASN cc_start: 0.8087 (m110) cc_final: 0.7722 (m110)
REVERT: B  171 GLU cc_start: 0.7753 (tt0) cc_final: 0.7026 (pt0)
REVERT: B  227 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: B  597 ASP cc_start: 0.7407 (m-30) cc_final: 0.6886 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 104
  average time/residue: 1.0740
  time to fit residues: 118.6940
Evaluate side-chains
  104 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  121 ASN
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 77 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.114930 restraints weight = 18417.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 3.40
r_work: 0.3129 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6748  Z= 0.226
  Angle     :  0.589   9.650   9171  Z= 0.289
  Chirality :  0.043   0.248    980
  Planarity :  0.004   0.066   1179
  Dihedral  :  6.826  57.445   1034
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.07 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.31), residues: 793
  helix:  0.80 (0.27), residues: 387
  sheet: -0.36 (0.72), residues: 57
  loop : -0.87 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.005   0.001   HIS B 374 
 PHE   0.012   0.001   PHE A 338 
 TYR   0.019   0.001   TYR B 385 
 ARG   0.006   0.000   ARG A 346 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  420 ASP cc_start: 0.8860 (m-30) cc_final: 0.8551 (m-30)
REVERT: A  444 LYS cc_start: 0.8173 (mtpt) cc_final: 0.7762 (mtpm)
REVERT: B   63 ASN cc_start: 0.8074 (m110) cc_final: 0.7708 (m110)
REVERT: B  171 GLU cc_start: 0.7697 (tt0) cc_final: 0.6961 (pt0)
REVERT: B  227 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: B  597 ASP cc_start: 0.7416 (m-30) cc_final: 0.6891 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 102
  average time/residue: 1.0620
  time to fit residues: 115.1960
Evaluate side-chains
  103 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  512 VAL
Chi-restraints excluded: chain B residue   74 LYS
Chi-restraints excluded: chain B residue   78 THR
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  212 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  347 THR
Chi-restraints excluded: chain B residue  401 HIS
Chi-restraints excluded: chain B residue  491 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0040
   chunk 65 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0970
   overall best weight:    0.3128

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN
A 506 GLN
B 159 ASN
B 522 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.155480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.119178 restraints weight = 18159.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 3.56
r_work: 0.3186 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6748  Z= 0.157
  Angle     :  0.550   9.633   9171  Z= 0.270
  Chirality :  0.042   0.247    980
  Planarity :  0.004   0.067   1179
  Dihedral  :  6.193  57.033   1034
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.79 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.31), residues: 793
  helix:  0.95 (0.28), residues: 379
  sheet: -0.29 (0.73), residues: 57
  loop : -0.88 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 566 
 HIS   0.004   0.001   HIS B 374 
 PHE   0.011   0.001   PHE B 327 
 TYR   0.018   0.001   TYR B 385 
 ARG   0.006   0.000   ARG A 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5032.77 seconds
wall clock time: 90 minutes 29.29 seconds (5429.29 seconds total)