Starting phenix.real_space_refine
on Tue Mar 11 19:20:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8whz_37553/03_2025/8whz_37553.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8whz_37553/03_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_37553/03_2025/8whz_37553.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8whz_37553/03_2025/8whz_37553.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8whz_37553/03_2025/8whz_37553.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8whz_37553/03_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-5624/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: 4.36, per 1000 atoms: 0.67
  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: 1.46
  Conformation dependent library (CDL) restraints added in 857.9 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: 0.58
  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: 1.56

  Time building geometry restraints manager: 1.77 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:             2.310
  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:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.110
  Find NCS groups from input model:        0.060
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.580
-------------------------------------------------------------------------------
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  : 0.667 
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: 0.2072
  time to fit residues: 53.4119
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  : 0.707 
-------------------------------------------------------------------------------
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 = 49)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.115386 restraints weight = 16045.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.118878 restraints weight = 8958.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.121301 restraints weight = 6061.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
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  : 0.673 
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: 0.6949 (mtp) cc_final: 0.6709 (mmm)
REVERT: A  176 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7097 (mm)
REVERT: A  243 TYR cc_start: 0.8907 (t80) cc_final: 0.8666 (t80)
REVERT: A  250 ASN cc_start: 0.8597 (t0) cc_final: 0.8387 (m110)
REVERT: A  323 MET cc_start: 0.8259 (mmt) cc_final: 0.7214 (mmm)
REVERT: A  360 MET cc_start: 0.8288 (ppp) cc_final: 0.7648 (ppp)
REVERT: A  366 MET cc_start: 0.8665 (ppp) cc_final: 0.7858 (ppp)
REVERT: A  594 TRP cc_start: 0.8061 (t-100) cc_final: 0.7819 (t-100)
REVERT: B  347 PHE cc_start: 0.6367 (m-80) cc_final: 0.5926 (m-80)
  outliers start: 17
  outliers final: 7
  residues processed: 137
  average time/residue: 0.1898
  time to fit residues: 34.6752
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  : 0.745 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 60 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0020
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6188

-------------------------------------------------------------------------------
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 373 HIS
A 472 GLN
A 508 ASN
B 417 ASN
B 493 GLN
B 505 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.142804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114208 restraints weight = 16035.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.117705 restraints weight = 8909.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.120036 restraints weight = 6017.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.4378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6702  Z= 0.198
  Angle     :  0.627   6.824   9110  Z= 0.329
  Chirality :  0.045   0.211    964
  Planarity :  0.005   0.048   1172
  Dihedral  :  5.568  45.448    984
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.94 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.82 %
    Favored  : 82.88 %
  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: -0.25 (0.29), residues: 787
  helix:  0.67 (0.25), residues: 406
  sheet:  0.23 (0.82), residues: 42
  loop : -1.21 (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   0.018   0.001   PHE A 369 
 TYR   0.016   0.002   TYR A 237 
 ARG   0.004   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
  142 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7092 (mtp) cc_final: 0.6642 (mmm)
REVERT: A  243 TYR cc_start: 0.8837 (t80) cc_final: 0.8584 (t80)
REVERT: A  310 GLU cc_start: 0.7861 (tp30) cc_final: 0.6704 (tp30)
REVERT: A  323 MET cc_start: 0.8447 (mmt) cc_final: 0.7236 (mmm)
REVERT: A  366 MET cc_start: 0.8604 (ppp) cc_final: 0.7887 (ppp)
REVERT: A  376 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7833 (tpt)
REVERT: A  441 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8374 (ttpp)
REVERT: A  472 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7414 (pm20)
REVERT: B  340 GLU cc_start: 0.6894 (mp0) cc_final: 0.6499 (mp0)
REVERT: B  347 PHE cc_start: 0.6455 (m-80) cc_final: 0.6175 (m-80)
REVERT: B  369 TYR cc_start: 0.7070 (m-80) cc_final: 0.6856 (m-80)
REVERT: B  417 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8404 (t0)
  outliers start: 16
  outliers final: 6
  residues processed: 136
  average time/residue: 0.1873
  time to fit residues: 33.6893
Evaluate side-chains
  113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
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  441 LYS
Chi-restraints excluded: chain A residue  445 THR
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  417 ASN
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:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 77 optimal weight:    0.3980
   chunk 72 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0010
   chunk 53 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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 472 GLN
A 508 ASN
A 598 GLN
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 505 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.142032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.114164 restraints weight = 16412.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.117455 restraints weight = 9267.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.119708 restraints weight = 6316.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.4971

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= 0.180
  Angle     :  0.597   6.609   9110  Z= 0.316
  Chirality :  0.044   0.208    964
  Planarity :  0.005   0.047   1172
  Dihedral  :  5.333  36.303    984
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.26 %
    Favored  : 81.29 %
  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: -0.08 (0.29), residues: 787
  helix:  0.82 (0.25), residues: 401
  sheet:  0.78 (0.81), residues: 40
  loop : -1.20 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 594 
 HIS   0.003   0.001   HIS A 374 
 PHE   0.031   0.001   PHE B 375 
 TYR   0.014   0.001   TYR A 199 
 ARG   0.003   0.000   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
  135 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  366 MET cc_start: 0.8576 (ppp) cc_final: 0.7927 (ppp)
REVERT: A  441 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8442 (ttpp)
REVERT: B  340 GLU cc_start: 0.6821 (mp0) cc_final: 0.6541 (mp0)
REVERT: B  347 PHE cc_start: 0.6221 (m-80) cc_final: 0.5687 (m-80)
REVERT: B  349 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8171 (p)
REVERT: B  406 GLU cc_start: 0.7808 (mp0) cc_final: 0.7544 (mp0)
  outliers start: 17
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1977
  time to fit residues: 33.9341
Evaluate side-chains
  111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
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  385 THR
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  453 TYR
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 149 ASN
** 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**
B 474 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.139576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.111766 restraints weight = 16208.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.114931 restraints weight = 9213.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.117128 restraints weight = 6322.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6702  Z= 0.219
  Angle     :  0.612   8.347   9110  Z= 0.323
  Chirality :  0.044   0.201    964
  Planarity :  0.005   0.045   1172
  Dihedral  :  5.221  37.116    984
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.83 %
    Favored  : 79.57 %
  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: -0.11 (0.29), residues: 787
  helix:  0.82 (0.25), residues: 400
  sheet:  0.24 (0.80), residues: 42
  loop : -1.17 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 473 
 HIS   0.006   0.001   HIS A 345 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.022   0.002   TYR A 243 
 ARG   0.007   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
  138 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 TRP cc_start: 0.8386 (t-100) cc_final: 0.7876 (t60)
REVERT: A  249 MET cc_start: 0.8361 (mtm) cc_final: 0.8015 (mtp)
REVERT: A  323 MET cc_start: 0.8411 (mmm) cc_final: 0.7043 (mmm)
REVERT: A  366 MET cc_start: 0.8576 (ppp) cc_final: 0.7908 (ppp)
REVERT: A  376 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7732 (tpt)
REVERT: A  406 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8530 (mm-30)
REVERT: A  441 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8493 (ttpp)
REVERT: A  461 TRP cc_start: 0.9047 (m-10) cc_final: 0.8697 (m-10)
REVERT: B  347 PHE cc_start: 0.6346 (m-80) cc_final: 0.6040 (m-80)
REVERT: B  349 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8344 (p)
REVERT: B  406 GLU cc_start: 0.7853 (mp0) cc_final: 0.7548 (mp0)
  outliers start: 25
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1788
  time to fit residues: 30.6976
Evaluate side-chains
  124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  250 ASN
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  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
Chi-restraints excluded: chain B residue  480 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    0.0670
   chunk 64 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 52 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0770
   chunk 73 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.3476

-------------------------------------------------------------------------------
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 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 = 0.4054 r_free = 0.4054 target = 0.141642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114212 restraints weight = 16005.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.117477 restraints weight = 9156.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119727 restraints weight = 6294.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6702  Z= 0.163
  Angle     :  0.587   6.603   9110  Z= 0.308
  Chirality :  0.043   0.201    964
  Planarity :  0.005   0.051   1172
  Dihedral  :  4.822  35.310    984
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.92 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.71 %
    Favored  : 77.27 %
  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:  0.06 (0.29), residues: 787
  helix:  0.93 (0.25), residues: 402
  sheet:  0.66 (0.77), residues: 41
  loop : -1.10 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   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   0.003   0.000   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
  140 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 MET cc_start: 0.7363 (mmm) cc_final: 0.7153 (mmt)
REVERT: A  163 TRP cc_start: 0.8421 (t-100) cc_final: 0.8112 (t60)
REVERT: A  190 MET cc_start: 0.8016 (ptp) cc_final: 0.7806 (ptp)
REVERT: A  234 LYS cc_start: 0.9352 (ptmm) cc_final: 0.9135 (ptpp)
REVERT: A  249 MET cc_start: 0.8389 (mtm) cc_final: 0.8106 (mtp)
REVERT: A  287 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6197 (pm20)
REVERT: A  323 MET cc_start: 0.8394 (mmm) cc_final: 0.6865 (mmm)
REVERT: A  366 MET cc_start: 0.8491 (ppp) cc_final: 0.7841 (ppp)
REVERT: A  376 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7768 (tpt)
REVERT: A  406 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8509 (mm-30)
REVERT: A  441 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8452 (ttpp)
REVERT: A  461 TRP cc_start: 0.9004 (m-10) cc_final: 0.8732 (m-10)
REVERT: B  340 GLU cc_start: 0.6843 (mp0) cc_final: 0.6411 (mp0)
REVERT: B  347 PHE cc_start: 0.6200 (m-80) cc_final: 0.5887 (m-80)
REVERT: B  481 LYS cc_start: 0.7765 (pptt) cc_final: 0.7419 (ptpp)
  outliers start: 21
  outliers final: 7
  residues processed: 138
  average time/residue: 0.1653
  time to fit residues: 31.3613
Evaluate side-chains
  112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
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  468 ILE
Chi-restraints excluded: chain B residue  362 VAL
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:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.136777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.108858 restraints weight = 16179.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.112000 restraints weight = 9039.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.114180 restraints weight = 6197.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.6175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6702  Z= 0.216
  Angle     :  0.613   9.296   9110  Z= 0.324
  Chirality :  0.044   0.189    964
  Planarity :  0.005   0.048   1172
  Dihedral  :  4.974  35.566    984
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.19 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.86 %
    Favored  : 75.25 %
  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:  0.09 (0.29), residues: 787
  helix:  0.92 (0.25), residues: 408
  sheet:  0.85 (0.75), residues: 40
  loop : -1.09 (0.32), residues: 339

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   0.023   0.002   PHE A 452 
 TYR   0.024   0.002   TYR A 199 
 ARG   0.006   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
  132 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.9001 (m110) cc_final: 0.8615 (m-40)
REVERT: A  163 TRP cc_start: 0.8513 (t-100) cc_final: 0.8268 (t60)
REVERT: A  234 LYS cc_start: 0.9373 (ptmm) cc_final: 0.9154 (ptpp)
REVERT: A  249 MET cc_start: 0.8419 (mtm) cc_final: 0.8156 (mtp)
REVERT: A  287 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6842 (pm20)
REVERT: A  306 ARG cc_start: 0.8474 (ttp-170) cc_final: 0.8193 (ttp-170)
REVERT: A  323 MET cc_start: 0.8431 (mmm) cc_final: 0.7014 (mmm)
REVERT: A  361 CYS cc_start: 0.5267 (OUTLIER) cc_final: 0.4993 (p)
REVERT: A  366 MET cc_start: 0.8529 (ppp) cc_final: 0.7824 (ppp)
REVERT: A  376 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7755 (tpt)
REVERT: A  406 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8616 (mm-30)
REVERT: A  441 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8481 (ttpp)
REVERT: A  461 TRP cc_start: 0.9040 (m-10) cc_final: 0.8761 (m-10)
  outliers start: 27
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1536
  time to fit residues: 26.0868
Evaluate side-chains
  115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  195 HIS
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 B residue  349 SER
Chi-restraints excluded: chain B residue  362 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
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:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 101 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 = 0.4004 r_free = 0.4004 target = 0.137962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.110009 restraints weight = 16055.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.113270 restraints weight = 8973.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.115418 restraints weight = 6122.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.6472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6702  Z= 0.206
  Angle     :  0.623   8.764   9110  Z= 0.329
  Chirality :  0.044   0.189    964
  Planarity :  0.004   0.045   1172
  Dihedral  :  4.943  35.604    984
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.81 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 22.73 %
    Favored  : 73.81 %
  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:  0.15 (0.29), residues: 787
  helix:  1.03 (0.26), residues: 402
  sheet:  0.83 (0.75), residues: 41
  loop : -1.12 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 473 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.033   0.002   PHE B 375 
 TYR   0.028   0.002   TYR A 199 
 ARG   0.006   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
  127 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.9038 (m110) cc_final: 0.8620 (m-40)
REVERT: A  152 MET cc_start: 0.7029 (mmt) cc_final: 0.6773 (mmm)
REVERT: A  163 TRP cc_start: 0.8591 (t-100) cc_final: 0.8298 (t60)
REVERT: A  234 LYS cc_start: 0.9414 (ptmm) cc_final: 0.9089 (pttp)
REVERT: A  243 TYR cc_start: 0.8717 (t80) cc_final: 0.8495 (t80)
REVERT: A  249 MET cc_start: 0.8431 (mtm) cc_final: 0.8163 (mtp)
REVERT: A  270 MET cc_start: 0.6736 (tpt) cc_final: 0.6437 (tpt)
REVERT: A  287 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6637 (pm20)
REVERT: A  306 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8227 (ttp-170)
REVERT: A  323 MET cc_start: 0.8419 (mmm) cc_final: 0.6936 (mmm)
REVERT: A  366 MET cc_start: 0.8504 (ppp) cc_final: 0.7793 (ppp)
REVERT: A  376 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7734 (tpt)
REVERT: A  406 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8640 (mm-30)
REVERT: A  441 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8472 (ttpp)
REVERT: A  560 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (mt)
  outliers start: 24
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1708
  time to fit residues: 28.6144
Evaluate side-chains
  118 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
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  318 VAL
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 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  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  455 LEU
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:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 44 optimal weight:    0.4980
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0060
   chunk 13 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.5996

-------------------------------------------------------------------------------
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 417 ASN
** 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 = 0.4011 r_free = 0.4011 target = 0.138211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.110755 restraints weight = 16203.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.113987 restraints weight = 9144.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.116192 restraints weight = 6228.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.6666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6702  Z= 0.194
  Angle     :  0.640   9.018   9110  Z= 0.334
  Chirality :  0.044   0.192    964
  Planarity :  0.004   0.046   1172
  Dihedral  :  4.829  34.856    984
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.56 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 23.31 %
    Favored  : 73.67 %
  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:  0.16 (0.30), residues: 787
  helix:  1.06 (0.26), residues: 402
  sheet:  0.76 (0.79), residues: 41
  loop : -1.13 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 473 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.015   0.001   PHE A 452 
 TYR   0.025   0.002   TYR A 199 
 ARG   0.005   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
  128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASN cc_start: 0.8998 (m110) cc_final: 0.8559 (m-40)
REVERT: A  152 MET cc_start: 0.6920 (mmt) cc_final: 0.6673 (mmm)
REVERT: A  234 LYS cc_start: 0.9391 (ptmm) cc_final: 0.9116 (pttp)
REVERT: A  243 TYR cc_start: 0.8676 (t80) cc_final: 0.8472 (t80)
REVERT: A  249 MET cc_start: 0.8450 (mtm) cc_final: 0.8191 (mtp)
REVERT: A  306 ARG cc_start: 0.8359 (ttp-170) cc_final: 0.8110 (ttp-170)
REVERT: A  323 MET cc_start: 0.8306 (mmm) cc_final: 0.6857 (mmm)
REVERT: A  366 MET cc_start: 0.8411 (ppp) cc_final: 0.7783 (ppp)
REVERT: A  376 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7777 (tpt)
REVERT: A  406 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8629 (mm-30)
REVERT: A  441 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8642 (ttpp)
REVERT: A  461 TRP cc_start: 0.9021 (m-10) cc_final: 0.8698 (m-10)
REVERT: A  560 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8819 (mt)
REVERT: A  578 ASN cc_start: 0.8679 (t0) cc_final: 0.8360 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 123
  average time/residue: 0.1528
  time to fit residues: 26.6120
Evaluate side-chains
  117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 GLN
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  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 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  401 VAL
Chi-restraints excluded: chain B residue  407 VAL
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 26 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0070
   chunk 39 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0770
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0030
   overall best weight:    0.2366

-------------------------------------------------------------------------------
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 417 ASN
** 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 = 0.4044 r_free = 0.4044 target = 0.140629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.113108 restraints weight = 16161.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.116354 restraints weight = 9118.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.118582 restraints weight = 6227.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.6902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6702  Z= 0.170
  Angle     :  0.662  11.116   9110  Z= 0.340
  Chirality :  0.044   0.197    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  4.605  31.682    984
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 25.47 %
    Favored  : 72.81 %
  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:  0.30 (0.30), residues: 787
  helix:  1.25 (0.26), residues: 392
  sheet:  1.06 (0.80), residues: 41
  loop : -1.14 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A 345 
 PHE   0.021   0.001   PHE A 592 
 TYR   0.021   0.001   TYR A 199 
 ARG   0.005   0.000   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
  125 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.7805 (ppp) cc_final: 0.7406 (ppp)
REVERT: A  121 ASN cc_start: 0.8989 (m110) cc_final: 0.8538 (m-40)
REVERT: A  152 MET cc_start: 0.7046 (mmt) cc_final: 0.6510 (mmm)
REVERT: A  234 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9098 (pttp)
REVERT: A  306 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.8051 (ttp-170)
REVERT: A  323 MET cc_start: 0.8346 (mmm) cc_final: 0.7046 (mmm)
REVERT: A  366 MET cc_start: 0.8273 (ppp) cc_final: 0.7742 (ppp)
REVERT: A  376 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7759 (tpt)
REVERT: A  441 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8694 (ttpp)
REVERT: A  461 TRP cc_start: 0.8993 (m-10) cc_final: 0.8663 (m-10)
REVERT: A  572 ASN cc_start: 0.8725 (t0) cc_final: 0.8238 (p0)
REVERT: A  578 ASN cc_start: 0.8620 (t0) cc_final: 0.8307 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1611
  time to fit residues: 27.7589
Evaluate side-chains
  110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  441 LYS
Chi-restraints excluded: chain A residue  472 GLN
Chi-restraints excluded: chain B residue  362 VAL
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  469 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    0.0010
   chunk 48 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0770
   chunk 76 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   overall best weight:    0.2342

-------------------------------------------------------------------------------
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**
** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.140576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.113247 restraints weight = 16347.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.116565 restraints weight = 9171.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.118655 restraints weight = 6216.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.6952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.338   6702  Z= 0.574
  Angle     :  1.156  59.166   9110  Z= 0.642
  Chirality :  0.050   0.634    964
  Planarity :  0.004   0.047   1172
  Dihedral  :  4.608  31.669    984
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 25.32 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.13 %
  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:  0.30 (0.30), residues: 787
  helix:  1.24 (0.26), residues: 393
  sheet:  1.07 (0.80), residues: 41
  loop : -1.12 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 477 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.014   0.001   PHE A 452 
 TYR   0.018   0.001   TYR A 199 
 ARG   0.010   0.000   ARG B 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2664.89 seconds
wall clock time: 46 minutes 45.61 seconds (2805.61 seconds total)