Starting phenix.real_space_refine
on Tue Feb 11 19:53:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/02_2025/8whz_37553.cif"
  }
  resolution = 3.93
  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=  -0.000 sd=   0.044
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     Cl      1      4.86       5
     C    4173      2.51       5
     N    1073      2.21       5
     O    1230      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: 6515
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
    Chain: "B"
      Number of atoms: 1559
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1559
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 13, 'TRANS': 180}
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.72, per 1000 atoms: 0.72
  Number of scatterers: 6515
  At special positions: 0
  Unit cell: (75.97, 95.23, 114.49, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      37     16.00
     O    1230      8.00
     N    1073      7.00
     C    4173      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=2.03
    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=2.03
    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
    NAG-ASN
      " NAG A 903 " - " ASN A 546 "
      " NAG A 904 " - " ASN A  90 "
      " NAG A 905 " - " ASN A 322 "
      " NAG A 906 " - " ASN A  53 "
      " NAG B 601 " - " ASN B 354 "
      " NAG B 602 " - " ASN B 343 "
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 890.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "


  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      57.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 52
      removed outlier: 3.795A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.802A  pdb=" N   VAL A 107 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.312A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      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 218 through 252
      removed outlier: 3.752A  pdb=" N   LEU A 222 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (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 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.918A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.743A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.685A  pdb=" N   ARG A 393 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.642A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.240A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    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 485
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
      removed outlier: 3.753A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.827A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.532A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.894A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.806A  pdb=" N   SER B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.788A  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 352
      removed outlier: 3.666A  pdb=" N   THR A 347 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 359 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.875A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 453
      removed outlier: 3.523A  pdb=" N   TYR B 453 " --> pdb=" O   GLN B 493 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    903 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: 1.59

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1864
        1.33 -     1.46: 1357
        1.46 -     1.58: 3422
        1.58 -     1.70: 1
        1.70 -     1.82: 58
  Bond restraints: 6702
  Sorted by residual:
  bond pdb=" C   THR A  27 "
       pdb=" N   PHE A  28 "
    ideal  model  delta    sigma   weight residual
    1.335  1.292  0.043 1.30e-02 5.92e+03 1.12e+01
  bond pdb=" N   THR A  27 "
       pdb=" CA  THR A  27 "
    ideal  model  delta    sigma   weight residual
    1.459  1.421  0.038 1.17e-02 7.31e+03 1.08e+01
  bond pdb=" CA  ARG B 457 "
       pdb=" CB  ARG B 457 "
    ideal  model  delta    sigma   weight residual
    1.534  1.480  0.053 1.78e-02 3.16e+03 8.94e+00
  bond pdb=" CA  THR A  27 "
       pdb=" C   THR A  27 "
    ideal  model  delta    sigma   weight residual
    1.524  1.492  0.032 1.24e-02 6.50e+03 6.85e+00
  bond pdb=" CB  PRO B 384 "
       pdb=" CG  PRO B 384 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.30e+00
  ... (remaining 6697 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 8753
        1.88 -     3.77: 312
        3.77 -     5.65: 37
        5.65 -     7.54: 6
        7.54 -     9.42: 2
  Bond angle restraints: 9110
  Sorted by residual:
  angle pdb=" N   LYS A 313 "
        pdb=" CA  LYS A 313 "
        pdb=" C   LYS A 313 "
      ideal   model   delta    sigma   weight residual
     111.82  106.74    5.08 1.16e+00 7.43e-01 1.92e+01
  angle pdb=" CA  PRO B 384 "
        pdb=" N   PRO B 384 "
        pdb=" CD  PRO B 384 "
      ideal   model   delta    sigma   weight residual
     112.00  106.33    5.67 1.40e+00 5.10e-01 1.64e+01
  angle pdb=" N   CYS A 498 "
        pdb=" CA  CYS A 498 "
        pdb=" C   CYS A 498 "
      ideal   model   delta    sigma   weight residual
     110.44  105.84    4.60 1.20e+00 6.94e-01 1.47e+01
  angle pdb=" CA  ARG B 457 "
        pdb=" C   ARG B 457 "
        pdb=" N   LYS B 458 "
      ideal   model   delta    sigma   weight residual
     115.61  120.89   -5.28 1.45e+00 4.76e-01 1.32e+01
  angle pdb=" N   VAL A 364 "
        pdb=" CA  VAL A 364 "
        pdb=" C   VAL A 364 "
      ideal   model   delta    sigma   weight residual
     106.21  109.67   -3.46 1.07e+00 8.73e-01 1.05e+01
  ... (remaining 9105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3628
       17.95 -    35.90: 318
       35.90 -    53.85: 58
       53.85 -    71.80: 17
       71.80 -    89.75: 8
  Dihedral angle restraints: 4029
    sinusoidal: 1705
      harmonic: 2324
  Sorted by residual:
  dihedral pdb=" CA  CYS B 361 "
           pdb=" C   CYS B 361 "
           pdb=" N   VAL B 362 "
           pdb=" CA  VAL B 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.36   36.64     0      5.00e+00 4.00e-02 5.37e+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  134.85  -41.85     1      1.00e+01 1.00e-02 2.45e+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  129.35  -36.35     1      1.00e+01 1.00e-02 1.87e+01
  ... (remaining 4026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 705
       0.049 -    0.097: 202
       0.097 -    0.146: 54
       0.146 -    0.194: 2
       0.194 -    0.243: 1
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG A 905 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 905 "
            pdb=" O5  NAG A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  PRO B 384 "
            pdb=" N   PRO B 384 "
            pdb=" C   PRO B 384 "
            pdb=" CB  PRO B 384 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality pdb=" CG  LEU B 492 "
            pdb=" CB  LEU B 492 "
            pdb=" CD1 LEU B 492 "
            pdb=" CD2 LEU B 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.83e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 383 "   -0.072 5.00e-02 4.00e+02   1.05e-01 1.78e+01
        pdb=" N   PRO B 384 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO B 384 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO B 384 "   -0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  69 "   -0.016 2.00e-02 2.50e+03   1.13e-02 3.22e+00
        pdb=" CG  TRP A  69 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  69 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  69 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  69 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  69 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  69 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  69 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  69 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 506 "    0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 507 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 507 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 507 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 45
        2.48 -     3.08: 4740
        3.08 -     3.69: 10301
        3.69 -     4.29: 14541
        4.29 -     4.90: 22781
  Nonbonded interactions: 52408
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 421 "
            pdb=" CZ  ARG B 457 "
     model   vdw
     1.873 3.270
  nonbonded pdb=" O   TYR B 421 "
            pdb=" NH1 ARG B 457 "
     model   vdw
     1.994 3.120
  nonbonded pdb=" NH2 ARG B 454 "
            pdb=" CG  ARG B 457 "
     model   vdw
     2.068 3.520
  nonbonded pdb=" O   LEU A 156 "
            pdb=" OH  TYR A 252 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" CZ  ARG B 454 "
            pdb=" NE  ARG B 457 "
     model   vdw
     2.171 3.350
  ... (remaining 52403 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.560
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.420
  Find NCS groups from input model:        0.050
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
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   0.091   6702  Z= 0.254
  Angle     :  0.791   9.421   9110  Z= 0.456
  Chirality :  0.047   0.243    964
  Planarity :  0.006   0.105   1172
  Dihedral  : 14.476  89.752   2516
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  0.29 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -0.54 (0.30), residues: 787
  helix:  0.61 (0.26), residues: 390
  sheet: -0.55 (0.89), residues: 35
  loop : -1.43 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  69 
 HIS   0.004   0.001   HIS A 493 
 PHE   0.014   0.002   PHE A 230 
 TYR   0.020   0.002   TYR A 454 
 ARG   0.006   0.001   ARG A 582 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6456 (mtp) cc_final: 0.6177 (mmm)
REVERT: A  243 TYR cc_start: 0.9040 (t80) cc_final: 0.8669 (t80)
REVERT: A  270 MET cc_start: 0.7170 (tpt) cc_final: 0.6916 (tpt)
REVERT: A  333 LEU cc_start: 0.9346 (mt) cc_final: 0.9130 (mm)
REVERT: A  408 MET cc_start: 0.8318 (mmp) cc_final: 0.8081 (mmt)
REVERT: A  461 TRP cc_start: 0.8963 (m-10) cc_final: 0.8732 (m-10)
REVERT: A  484 ILE cc_start: 0.8728 (mm) cc_final: 0.8257 (tp)
REVERT: B  406 GLU cc_start: 0.8224 (mp0) cc_final: 0.8015 (mp0)
  outliers start: 2
  outliers final: 1
  residues processed: 202
  average time/residue: 0.2149
  time to fit residues: 55.1874
Evaluate side-chains
  124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  60 GLN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
B 417 ASN
B 505 HIS
** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.143753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115416 restraints weight = 16045.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.118866 restraints weight = 8943.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.121271 restraints weight = 6070.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6702  Z= 0.252
  Angle     :  0.688   7.665   9110  Z= 0.360
  Chirality :  0.046   0.217    964
  Planarity :  0.005   0.054   1172
  Dihedral  :  6.010  51.658    985
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 11.08 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.33 (0.29), residues: 787
  helix:  0.64 (0.25), residues: 406
  sheet: -0.33 (0.80), residues: 42
  loop : -1.22 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 165 
 HIS   0.005   0.001   HIS A 417 
 PHE   0.033   0.002   PHE B 375 
 TYR   0.021   0.002   TYR B 421 
 ARG   0.009   0.001   ARG B 346 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.6953 (mtp) cc_final: 0.6712 (mmm)
REVERT: A  176 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7096 (mm)
REVERT: A  243 TYR cc_start: 0.8909 (t80) cc_final: 0.8666 (t80)
REVERT: A  250 ASN cc_start: 0.8598 (t0) cc_final: 0.8388 (m110)
REVERT: A  323 MET cc_start: 0.8256 (mmt) cc_final: 0.7215 (mmm)
REVERT: A  360 MET cc_start: 0.8287 (ppp) cc_final: 0.7649 (ppp)
REVERT: A  366 MET cc_start: 0.8666 (ppp) cc_final: 0.7861 (ppp)
REVERT: A  594 TRP cc_start: 0.8065 (t-100) cc_final: 0.7822 (t-100)
REVERT: B  347 PHE cc_start: 0.6364 (m-80) cc_final: 0.5923 (m-80)
  outliers start: 17
  outliers final: 7
  residues processed: 137
  average time/residue: 0.1835
  time to fit residues: 33.6116
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  517 THR
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
A 508 ASN
B 417 ASN
B 505 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.141788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.113173 restraints weight = 16089.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.116589 restraints weight = 8969.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.118826 restraints weight = 6083.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.4434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6702  Z= 0.213
  Angle     :  0.634   6.846   9110  Z= 0.335
  Chirality :  0.045   0.209    964
  Planarity :  0.005   0.050   1172
  Dihedral  :  5.755  47.168    984
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.19 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.53 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.28 (0.29), residues: 787
  helix:  0.64 (0.25), residues: 406
  sheet:  0.17 (0.82), residues: 42
  loop : -1.22 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.019   0.002   PHE A 369 
 TYR   0.015   0.002   TYR A 237 
 ARG   0.003   0.001   ARG A 582 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7169 (mtp) cc_final: 0.6760 (mmm)
REVERT: A  243 TYR cc_start: 0.8862 (t80) cc_final: 0.8623 (t80)
REVERT: A  323 MET cc_start: 0.8441 (mmt) cc_final: 0.7096 (mmm)
REVERT: A  333 LEU cc_start: 0.9059 (mt) cc_final: 0.8737 (mm)
REVERT: A  366 MET cc_start: 0.8664 (ppp) cc_final: 0.7875 (ppp)
REVERT: A  376 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7792 (tpt)
REVERT: B  340 GLU cc_start: 0.7021 (mp0) cc_final: 0.6643 (mp0)
REVERT: B  347 PHE cc_start: 0.6476 (m-80) cc_final: 0.6214 (m-80)
REVERT: B  369 TYR cc_start: 0.7129 (m-80) cc_final: 0.6897 (m-80)
  outliers start: 17
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1919
  time to fit residues: 33.5518
Evaluate side-chains
  107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0010
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 HIS
A 378 HIS
A 472 GLN
A 508 ASN
A 598 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.141343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.113320 restraints weight = 16349.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.116622 restraints weight = 9145.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.118948 restraints weight = 6196.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.5080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6702  Z= 0.179
  Angle     :  0.601   6.624   9110  Z= 0.317
  Chirality :  0.044   0.208    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  5.324  36.737    984
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 16.69 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.00 (0.29), residues: 787
  helix:  0.90 (0.25), residues: 401
  sheet:  0.89 (0.81), residues: 40
  loop : -1.18 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.032   0.001   PHE B 375 
 TYR   0.014   0.001   TYR A 199 
 ARG   0.004   0.001   ARG A 219 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  270 MET cc_start: 0.6956 (tpt) cc_final: 0.6496 (tpt)
REVERT: A  366 MET cc_start: 0.8581 (ppp) cc_final: 0.7938 (ppp)
REVERT: A  441 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8426 (ttpp)
REVERT: A  467 GLU cc_start: 0.8282 (pm20) cc_final: 0.7189 (pm20)
REVERT: B  347 PHE cc_start: 0.6203 (m-80) cc_final: 0.5700 (m-80)
REVERT: B  349 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8196 (p)
REVERT: B  406 GLU cc_start: 0.7922 (mp0) cc_final: 0.7669 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 123
  average time/residue: 0.1852
  time to fit residues: 30.5277
Evaluate side-chains
  109 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.0870
   chunk 13 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   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  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 378 HIS
A 380 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.140560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.112854 restraints weight = 16169.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.116086 restraints weight = 9137.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.118317 restraints weight = 6247.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.5503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6702  Z= 0.189
  Angle     :  0.603   8.516   9110  Z= 0.317
  Chirality :  0.044   0.205    964
  Planarity :  0.005   0.049   1172
  Dihedral  :  5.071  36.145    984
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.43 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 18.42 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.29), residues: 787
  helix:  0.82 (0.25), residues: 407
  sheet:  0.86 (0.78), residues: 40
  loop : -1.17 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.017   0.001   PHE B 490 
 TYR   0.022   0.002   TYR A 243 
 ARG   0.006   0.001   ARG B 346 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 TRP cc_start: 0.8392 (t-100) cc_final: 0.7890 (t60)
REVERT: A  243 TYR cc_start: 0.8599 (t80) cc_final: 0.8357 (t80)
REVERT: A  249 MET cc_start: 0.8304 (mtt) cc_final: 0.8006 (mmm)
REVERT: A  323 MET cc_start: 0.8413 (mmm) cc_final: 0.7286 (mmm)
REVERT: A  361 CYS cc_start: 0.4983 (OUTLIER) cc_final: 0.4722 (p)
REVERT: A  366 MET cc_start: 0.8590 (ppp) cc_final: 0.7933 (ppp)
REVERT: A  376 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7866 (tpp)
REVERT: A  406 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8485 (mm-30)
REVERT: A  441 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8460 (ttpp)
REVERT: B  347 PHE cc_start: 0.6186 (m-80) cc_final: 0.5858 (m-80)
REVERT: B  349 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8257 (p)
REVERT: B  406 GLU cc_start: 0.7824 (mp0) cc_final: 0.7549 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 123
  average time/residue: 0.1837
  time to fit residues: 30.9118
Evaluate side-chains
  118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0970
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0040
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0010
   chunk 73 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 378 HIS
A 472 GLN
B 439 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.141857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.114657 restraints weight = 15947.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.117951 restraints weight = 9102.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.119909 restraints weight = 6222.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6702  Z= 0.163
  Angle     :  0.598   8.579   9110  Z= 0.312
  Chirality :  0.043   0.200    964
  Planarity :  0.004   0.045   1172
  Dihedral  :  4.794  34.393    984
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.86 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.03 (0.29), residues: 787
  helix:  0.82 (0.25), residues: 408
  sheet:  0.75 (0.77), residues: 41
  loop : -1.15 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP A 473 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.033   0.001   PHE B 375 
 TYR   0.016   0.001   TYR A 199 
 ARG   0.004   0.001   ARG B 457 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8963 (m110) cc_final: 0.8568 (m-40)
REVERT: A  152 MET cc_start: 0.7460 (mmm) cc_final: 0.7205 (mmt)
REVERT: A  163 TRP cc_start: 0.8424 (t-100) cc_final: 0.8109 (t60)
REVERT: A  249 MET cc_start: 0.8204 (mtt) cc_final: 0.7845 (mmm)
REVERT: A  287 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6163 (pm20)
REVERT: A  323 MET cc_start: 0.8336 (mmm) cc_final: 0.6778 (mmm)
REVERT: A  361 CYS cc_start: 0.4888 (OUTLIER) cc_final: 0.4626 (p)
REVERT: A  366 MET cc_start: 0.8461 (ppp) cc_final: 0.7824 (ppp)
REVERT: A  376 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7749 (tpt)
REVERT: A  406 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: A  441 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8463 (ttpp)
REVERT: A  461 TRP cc_start: 0.8983 (m-10) cc_final: 0.8711 (m-10)
REVERT: A  462 MET cc_start: 0.8596 (mtm) cc_final: 0.8346 (mtm)
REVERT: B  347 PHE cc_start: 0.6037 (m-80) cc_final: 0.5675 (m-80)
REVERT: B  349 SER cc_start: 0.8489 (OUTLIER) cc_final: 0.8107 (p)
  outliers start: 22
  outliers final: 6
  residues processed: 123
  average time/residue: 0.1565
  time to fit residues: 27.3048
Evaluate side-chains
  107 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0020
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5366

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.139839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.112500 restraints weight = 16087.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.115678 restraints weight = 9167.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.117886 restraints weight = 6292.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.6121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6702  Z= 0.178
  Angle     :  0.605   9.525   9110  Z= 0.315
  Chirality :  0.043   0.193    964
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.764  33.032    984
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.29 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.02 (0.29), residues: 787
  helix:  0.90 (0.26), residues: 407
  sheet:  0.81 (0.77), residues: 41
  loop : -1.18 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.015   0.001   PHE B 490 
 TYR   0.024   0.001   TYR A 199 
 ARG   0.004   0.001   ARG B 457 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8989 (m110) cc_final: 0.8581 (m-40)
REVERT: A  163 TRP cc_start: 0.8488 (t-100) cc_final: 0.8281 (t60)
REVERT: A  243 TYR cc_start: 0.8610 (t80) cc_final: 0.8325 (t80)
REVERT: A  249 MET cc_start: 0.8155 (mtt) cc_final: 0.7789 (mmm)
REVERT: A  306 ARG cc_start: 0.8497 (ttp-170) cc_final: 0.8219 (ttp-170)
REVERT: A  323 MET cc_start: 0.8390 (mmm) cc_final: 0.6933 (mmm)
REVERT: A  361 CYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4527 (p)
REVERT: A  366 MET cc_start: 0.8486 (ppp) cc_final: 0.7809 (ppp)
REVERT: A  376 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7724 (tpt)
REVERT: A  406 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8570 (mm-30)
REVERT: A  441 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8493 (ttpp)
REVERT: A  471 ASP cc_start: 0.8710 (p0) cc_final: 0.8370 (p0)
REVERT: A  560 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8715 (mt)
REVERT: B  347 PHE cc_start: 0.6089 (m-80) cc_final: 0.5863 (m-80)
REVERT: B  349 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8160 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 123
  average time/residue: 0.1506
  time to fit residues: 26.1172
Evaluate side-chains
  116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 32 optimal weight:    8.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.138245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.110827 restraints weight = 16093.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.113932 restraints weight = 9178.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.116019 restraints weight = 6330.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.6454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6702  Z= 0.187
  Angle     :  0.593   6.617   9110  Z= 0.312
  Chirality :  0.043   0.188    964
  Planarity :  0.005   0.046   1172
  Dihedral  :  4.750  32.465    984
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.45 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.30), residues: 787
  helix:  0.96 (0.26), residues: 407
  sheet:  0.84 (0.75), residues: 41
  loop : -1.17 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  69 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.031   0.001   PHE B 375 
 TYR   0.020   0.001   TYR A 199 
 ARG   0.008   0.001   ARG B 457 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.9013 (m110) cc_final: 0.8587 (m-40)
REVERT: A  152 MET cc_start: 0.6865 (mmt) cc_final: 0.6458 (mmm)
REVERT: A  163 TRP cc_start: 0.8485 (t-100) cc_final: 0.8278 (t60)
REVERT: A  249 MET cc_start: 0.8170 (mtt) cc_final: 0.7812 (mmm)
REVERT: A  287 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6450 (pm20)
REVERT: A  306 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8138 (ttp-170)
REVERT: A  323 MET cc_start: 0.8369 (mmm) cc_final: 0.6917 (mmm)
REVERT: A  361 CYS cc_start: 0.4945 (OUTLIER) cc_final: 0.4705 (p)
REVERT: A  366 MET cc_start: 0.8403 (ppp) cc_final: 0.7751 (ppp)
REVERT: A  376 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7744 (tpt)
REVERT: A  406 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8607 (mm-30)
REVERT: A  441 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8623 (ttpp)
REVERT: A  461 TRP cc_start: 0.9016 (m-10) cc_final: 0.8715 (m-10)
REVERT: A  560 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8754 (mt)
REVERT: A  572 ASN cc_start: 0.8635 (t0) cc_final: 0.8376 (p0)
REVERT: A  591 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1540
  time to fit residues: 26.1280
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 70 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0270
   chunk 11 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.0642

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.134944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.107109 restraints weight = 16236.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.110215 restraints weight = 9204.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.112244 restraints weight = 6305.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.6865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6702  Z= 0.246
  Angle     :  0.654   7.767   9110  Z= 0.344
  Chirality :  0.045   0.184    964
  Planarity :  0.005   0.052   1172
  Dihedral  :  5.197  34.606    984
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.17 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.01 (0.29), residues: 787
  helix:  0.92 (0.26), residues: 404
  sheet:  0.42 (0.75), residues: 43
  loop : -1.14 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 473 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.022   0.002   PHE A 464 
 TYR   0.022   0.002   TYR A 199 
 ARG   0.009   0.001   ARG B 457 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7942 (ppp) cc_final: 0.7430 (ppp)
REVERT: A  121 ASN cc_start: 0.9022 (m110) cc_final: 0.8707 (m-40)
REVERT: A  152 MET cc_start: 0.7422 (mmt) cc_final: 0.6933 (mmm)
REVERT: A  163 TRP cc_start: 0.8569 (t-100) cc_final: 0.8294 (t60)
REVERT: A  249 MET cc_start: 0.8307 (mtt) cc_final: 0.7877 (mmm)
REVERT: A  280 SER cc_start: 0.8887 (m) cc_final: 0.8665 (p)
REVERT: A  306 ARG cc_start: 0.8507 (ttp-170) cc_final: 0.8139 (ttp-170)
REVERT: A  323 MET cc_start: 0.8496 (mmm) cc_final: 0.7086 (mmm)
REVERT: A  366 MET cc_start: 0.8578 (ppp) cc_final: 0.7867 (ppp)
REVERT: A  376 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7822 (tpt)
REVERT: A  406 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8670 (mm-30)
REVERT: A  441 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8542 (ttpp)
REVERT: A  461 TRP cc_start: 0.9023 (m-10) cc_final: 0.8710 (m-10)
REVERT: A  512 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8340 (t80)
REVERT: A  560 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8919 (mt)
REVERT: A  572 ASN cc_start: 0.8638 (t0) cc_final: 0.8361 (p0)
  outliers start: 27
  outliers final: 17
  residues processed: 123
  average time/residue: 0.1666
  time to fit residues: 28.2665
Evaluate side-chains
  121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  469 SER
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0770
   chunk 74 optimal weight:    0.0020
   chunk 39 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0470
   chunk 30 optimal weight:    0.0050
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.1258

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.140009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.113140 restraints weight = 16243.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.116233 restraints weight = 9142.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.118425 restraints weight = 6231.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.6996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6702  Z= 0.161
  Angle     :  0.641   9.613   9110  Z= 0.327
  Chirality :  0.043   0.195    964
  Planarity :  0.004   0.049   1172
  Dihedral  :  4.635  31.601    984
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.18 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 24.89 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: 787
  helix:  1.02 (0.26), residues: 405
  sheet:  0.66 (0.84), residues: 39
  loop : -1.11 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 345 
 PHE   0.033   0.001   PHE A 464 
 TYR   0.020   0.001   TYR A 199 
 ARG   0.008   0.001   ARG B 457 

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

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

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1574 Ramachandran restraints generated.
    787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7738 (ppp) cc_final: 0.7338 (ppp)
REVERT: A  121 ASN cc_start: 0.8990 (m110) cc_final: 0.8514 (m-40)
REVERT: A  152 MET cc_start: 0.7270 (mmt) cc_final: 0.6856 (mmm)
REVERT: A  163 TRP cc_start: 0.8527 (t-100) cc_final: 0.8309 (t60)
REVERT: A  234 LYS cc_start: 0.9418 (ptmm) cc_final: 0.9199 (pttp)
REVERT: A  249 MET cc_start: 0.8234 (mtt) cc_final: 0.7911 (mmm)
REVERT: A  287 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6622 (pm20)
REVERT: A  306 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8139 (ttp-170)
REVERT: A  323 MET cc_start: 0.8252 (mmm) cc_final: 0.6898 (mmm)
REVERT: A  366 MET cc_start: 0.8153 (ppp) cc_final: 0.7739 (ppp)
REVERT: A  376 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7710 (tpt)
REVERT: A  441 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8576 (ttpp)
REVERT: A  461 TRP cc_start: 0.8976 (m-10) cc_final: 0.8650 (m-10)
REVERT: A  512 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8310 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1678
  time to fit residues: 28.0875
Evaluate side-chains
  108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  271 TRP
Chi-restraints excluded: chain A residue  287 GLN
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  512 PHE
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  469 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.0970
   chunk 48 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 37 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 287 GLN
A 472 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.138992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.111690 restraints weight = 16324.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.114945 restraints weight = 9117.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.117138 restraints weight = 6137.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.7120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6702  Z= 0.177
  Angle     :  0.684  12.116   9110  Z= 0.348
  Chirality :  0.044   0.189    964
  Planarity :  0.004   0.049   1172
  Dihedral  :  4.694  28.119    984
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.30 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 24.89 %
    Favored  : 73.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  0.18 (0.30), residues: 787
  helix:  1.00 (0.26), residues: 402
  sheet:  0.92 (0.82), residues: 41
  loop : -1.02 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 594 
 HIS   0.004   0.001   HIS A 374 
 PHE   0.033   0.002   PHE B 375 
 TYR   0.023   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 482 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2557.71 seconds
wall clock time: 47 minutes 3.28 seconds (2823.28 seconds total)