Starting phenix.real_space_refine
on Fri Jan 17 08:31:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xn2_38495/01_2025/8xn2_38495.cif"
  }
  resolution = 2.79
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4872 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     C    4175      2.51       5
     N    1074      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6527
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
      Conformer: "B"
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
          bond proxies already assigned to first conformer: 4987
    Chain: "B"
      Number of atoms: 1545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1545
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 13, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 71
          Unusual residues: {' ZN': 1, 'NAG': 5}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A  34 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  34 " occ=0.50
  Time building chain proxies: 10.41, per 1000 atoms: 1.59
  Number of scatterers: 6527
  At special positions: 0
  Unit cell: (84.032, 78.376, 117.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      37     16.00
     O    1240      8.00
     N    1074      7.00
     C    4175      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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
    NAG-ASN
      " NAG A 701 " - " ASN A  53 "
      " NAG A 702 " - " ASN A 103 "
      " NAG A 703 " - " ASN A 432 "
      " NAG A 704 " - " ASN A 546 "
      " NAG A 705 " - " ASN A 322 "
      " NAG C   1 " - " ASN A  90 "
  Time building additional restraints: 1.65
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 706 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 706 " - pdb=" NE2 HIS A 378 "


  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      56.6% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.985A  pdb=" N   ASP A  38 " --> pdb=" O  AHIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.693A  pdb=" N   GLN A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
    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 92 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 4.072A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.288A  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 220 through 252
      removed outlier: 3.605A  pdb=" N   GLU A 224 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 279
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.644A  pdb=" N   PHE A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.646A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 447
      removed outlier: 3.511A  pdb=" N   GLU A 435 " --> pdb=" O   ASP A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 4.077A  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 484
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.185A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.580A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 542'
    Processing helix  chain 'A' and resid 547 through 561
      removed outlier: 3.525A  pdb=" N   GLY A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 560 " --> pdb=" O   ASN A 556 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY A 561 " --> pdb=" O   MET A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'B' and resid 337 through 342
    Processing helix  chain 'B' and resid 365 through 371
    Processing helix  chain 'B' and resid 384 through 388
      removed outlier: 3.617A  pdb=" N   LEU B 387 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 384 through 388'
    Processing helix  chain 'B' and resid 404 through 408
      removed outlier: 3.760A  pdb=" N   SER B 408 " --> pdb=" O   ASN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 134
      removed outlier: 6.967A  pdb=" N   GLU A 140 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.195A  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: 6.467A  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: 3.526A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 399 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 376 " --> pdb=" O   ALA B 435 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.680A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    925 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: 1.73

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2068
        1.34 -     1.46: 1419
        1.46 -     1.58: 3167
        1.58 -     1.70: 0
        1.70 -     1.81: 58
  Bond restraints: 6712
  Sorted by residual:
  bond pdb=" C   ASN A  33 "
       pdb=" N  BHIS A  34 "
    ideal  model  delta    sigma   weight residual
    1.335  1.393 -0.058 1.38e-02 5.25e+03 1.75e+01
  bond pdb=" N   THR A  20 "
       pdb=" CA  THR A  20 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.031 1.15e-02 7.56e+03 7.42e+00
  bond pdb=" N   GLN A 102 "
       pdb=" CA  GLN A 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.42e-02 4.96e+03 5.47e+00
  bond pdb=" N   LEU A  91 "
       pdb=" CA  LEU A  91 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.03e+00
  bond pdb=" C  BHIS A  34 "
       pdb=" N   GLU A  35 "
    ideal  model  delta    sigma   weight residual
    1.334  1.303  0.032 1.43e-02 4.89e+03 4.92e+00
  ... (remaining 6707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 8965
        2.09 -     4.18: 141
        4.18 -     6.27: 20
        6.27 -     8.36: 1
        8.36 -    10.45: 1
  Bond angle restraints: 9128
  Sorted by residual:
  angle pdb=" C   ILE A  21 "
        pdb=" N   GLU A  22 "
        pdb=" CA  GLU A  22 "
      ideal   model   delta    sigma   weight residual
     120.29  109.84   10.45 1.42e+00 4.96e-01 5.42e+01
  angle pdb=" C   ASN A 103 "
        pdb=" N   GLY A 104 "
        pdb=" CA  GLY A 104 "
      ideal   model   delta    sigma   weight residual
     120.14  115.08    5.06 1.25e+00 6.40e-01 1.64e+01
  angle pdb=" C   ASN A  33 "
        pdb=" N  BHIS A  34 "
        pdb=" CA BHIS A  34 "
      ideal   model   delta    sigma   weight residual
     120.31  114.77    5.54 1.52e+00 4.33e-01 1.33e+01
  angle pdb=" N   GLN A 102 "
        pdb=" CA  GLN A 102 "
        pdb=" C   GLN A 102 "
      ideal   model   delta    sigma   weight residual
     113.19  108.90    4.29 1.19e+00 7.06e-01 1.30e+01
  angle pdb=" O   ASN A  33 "
        pdb=" C   ASN A  33 "
        pdb=" N  BHIS A  34 "
      ideal   model   delta    sigma   weight residual
     122.07  125.67   -3.60 1.03e+00 9.43e-01 1.22e+01
  ... (remaining 9123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.15: 3804
       21.15 -    42.31: 212
       42.31 -    63.46: 24
       63.46 -    84.61: 22
       84.61 -   105.77: 5
  Dihedral angle restraints: 4067
    sinusoidal: 1739
      harmonic: 2328
  Sorted by residual:
  dihedral pdb=" CB  CYS A 530 "
           pdb=" SG  CYS A 530 "
           pdb=" SG  CYS A 542 "
           pdb=" CB  CYS A 542 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.72   55.72     1      1.00e+01 1.00e-02 4.19e+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  125.90  -32.90     1      1.00e+01 1.00e-02 1.54e+01
  dihedral pdb=" CA  SER B 494 "
           pdb=" C   SER B 494 "
           pdb=" N   TYR B 495 "
           pdb=" CA  TYR B 495 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.43   18.57     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 4064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.169: 973
       0.169 -    0.338: 4
       0.338 -    0.508: 0
       0.508 -    0.677: 1
       0.677 -    0.846: 1
  Chirality restraints: 979
  Sorted by residual:
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 3.08e+01
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 2.85e+01
  chirality pdb=" C1  NAG A 702 "
            pdb=" ND2 ASN A 103 "
            pdb=" C2  NAG A 702 "
            pdb=" O5  NAG A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.55   -0.85 2.00e-01 2.50e+01 1.79e+01
  ... (remaining 976 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "    0.338 2.00e-02 2.50e+03   2.92e-01 1.06e+03
        pdb=" C7  NAG C   1 "   -0.081 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "    0.048 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "   -0.510 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.204 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 703 "   -0.307 2.00e-02 2.50e+03   2.64e-01 8.68e+02
        pdb=" C7  NAG A 703 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG A 703 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2  NAG A 703 "    0.450 2.00e-02 2.50e+03
        pdb=" O7  NAG A 703 "   -0.214 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 702 "    0.154 2.00e-02 2.50e+03   1.27e-01 2.02e+02
        pdb=" C7  NAG A 702 "   -0.042 2.00e-02 2.50e+03
        pdb=" C8  NAG A 702 "    0.114 2.00e-02 2.50e+03
        pdb=" N2  NAG A 702 "   -0.205 2.00e-02 2.50e+03
        pdb=" O7  NAG A 702 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 704
        2.74 -     3.28: 6529
        3.28 -     3.82: 11456
        3.82 -     4.36: 13312
        4.36 -     4.90: 22587
  Nonbonded interactions: 54588
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 217 "
            pdb=" OD2 ASP A 225 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER B 514 "
            pdb=" OE2 GLU B 516 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 706 "
     model   vdw
     2.275 2.230
  nonbonded pdb=" NH1 ARG B 457 "
            pdb=" O   SER B 459 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" NE2 HIS A 374 "
            pdb=" OE1 GLU A 402 "
     model   vdw
     2.307 3.120
  ... (remaining 54583 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             33.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     26.610
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  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:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6033
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   0.058   6712  Z= 0.238
  Angle     :  0.631  10.454   9128  Z= 0.366
  Chirality :  0.056   0.846    979
  Planarity :  0.013   0.292   1172
  Dihedral  : 14.752 105.768   2552
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.30), residues: 790
  helix:  1.86 (0.27), residues: 394
  sheet:  1.73 (0.79), residues: 37
  loop : -0.30 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.011   0.002   HIS A 378 
 PHE   0.016   0.001   PHE A 592 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.001   0.000   ARG A 219 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7381 (mt0) cc_final: 0.7016 (mt0)
REVERT: A   62 MET cc_start: 0.6792 (ttt) cc_final: 0.6481 (ttp)
REVERT: A   63 ASN cc_start: 0.7254 (m-40) cc_final: 0.6920 (m-40)
REVERT: A   69 TRP cc_start: 0.7343 (t-100) cc_final: 0.6981 (t-100)
REVERT: A   79 LEU cc_start: 0.7823 (mt) cc_final: 0.7617 (tt)
REVERT: A  166 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6495 (tm-30)
REVERT: A  181 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5868 (mm-30)
REVERT: A  249 MET cc_start: 0.6946 (ttm) cc_final: 0.6529 (tmt)
REVERT: A  309 LYS cc_start: 0.6899 (mmtt) cc_final: 0.6684 (tppp)
REVERT: A  315 PHE cc_start: 0.7713 (m-80) cc_final: 0.7433 (m-80)
REVERT: A  320 LEU cc_start: 0.7688 (mt) cc_final: 0.7375 (mp)
REVERT: A  324 THR cc_start: 0.6941 (m) cc_final: 0.6660 (p)
REVERT: A  327 PHE cc_start: 0.6935 (t80) cc_final: 0.6700 (t80)
REVERT: A  330 ASN cc_start: 0.7527 (m-40) cc_final: 0.6911 (m110)
REVERT: A  349 TRP cc_start: 0.7630 (m100) cc_final: 0.7236 (m100)
REVERT: A  362 THR cc_start: 0.6829 (m) cc_final: 0.6107 (m)
REVERT: A  382 ASP cc_start: 0.7116 (m-30) cc_final: 0.6681 (m-30)
REVERT: A  385 TYR cc_start: 0.7179 (p90) cc_final: 0.6884 (p90)
REVERT: A  400 PHE cc_start: 0.7039 (m-10) cc_final: 0.6772 (m-80)
REVERT: A  408 MET cc_start: 0.7077 (mmt) cc_final: 0.6822 (mmt)
REVERT: A  441 LYS cc_start: 0.6470 (tttt) cc_final: 0.6172 (ttpp)
REVERT: A  462 MET cc_start: 0.6474 (mtt) cc_final: 0.5524 (mtm)
REVERT: A  465 LYS cc_start: 0.7999 (mttp) cc_final: 0.7461 (mttt)
REVERT: A  467 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6478 (mp0)
REVERT: A  477 TRP cc_start: 0.5159 (t-100) cc_final: 0.4787 (t-100)
REVERT: A  480 MET cc_start: 0.6110 (mtm) cc_final: 0.5858 (mtp)
REVERT: A  482 ARG cc_start: 0.6322 (ttm170) cc_final: 0.5996 (ttm-80)
REVERT: A  489 GLU cc_start: 0.6397 (pm20) cc_final: 0.5907 (pm20)
REVERT: A  499 ASP cc_start: 0.7568 (m-30) cc_final: 0.7315 (m-30)
REVERT: A  559 ARG cc_start: 0.7481 (ptm-80) cc_final: 0.7217 (ppp80)
REVERT: A  562 LYS cc_start: 0.7612 (mtpt) cc_final: 0.7326 (mtmt)
REVERT: A  577 LYS cc_start: 0.7744 (mttp) cc_final: 0.7203 (mtpt)
REVERT: A  582 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6818 (tpm-80)
REVERT: A  603 PHE cc_start: 0.6363 (t80) cc_final: 0.5897 (t80)
REVERT: A  606 TRP cc_start: 0.7584 (p90) cc_final: 0.7199 (p90)
REVERT: A  611 SER cc_start: 0.7182 (m) cc_final: 0.6863 (p)
REVERT: B  407 VAL cc_start: 0.7943 (t) cc_final: 0.7450 (m)
REVERT: B  414 GLN cc_start: 0.7559 (mm110) cc_final: 0.7240 (mm110)
REVERT: B  424 LYS cc_start: 0.7256 (tppt) cc_final: 0.6979 (tttt)
REVERT: B  468 ILE cc_start: 0.7771 (pt) cc_final: 0.7349 (mt)
REVERT: B  512 VAL cc_start: 0.7038 (t) cc_final: 0.6815 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 1.0280
  time to fit residues: 248.0457
Evaluate side-chains
  178 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    0.1980
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.0010
   chunk 23 optimal weight:    0.0870
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0020
   overall best weight:    0.1372

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

Flipped N/Q/H residues before XYZ refinement:
A  34 HIS    A
A 117 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 GLN
A 397 ASN
A 493 HIS
B 343 ASN
B 437 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.165595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.145243 restraints weight = 19165.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 3.29
r_work: 0.3851 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6712  Z= 0.196
  Angle     :  0.632  13.104   9128  Z= 0.317
  Chirality :  0.044   0.232    979
  Planarity :  0.004   0.041   1172
  Dihedral  :  8.410  74.206   1026
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.52 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.30), residues: 790
  helix:  1.78 (0.26), residues: 391
  sheet:  0.80 (0.71), residues: 49
  loop : -0.13 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 163 
 HIS   0.005   0.001   HIS A 378 
 PHE   0.025   0.002   PHE B 497 
 TYR   0.028   0.002   TYR A 385 
 ARG   0.003   0.000   ARG A 204 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 196
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7924 (m-40) cc_final: 0.7659 (m-40)
REVERT: A   68 LYS cc_start: 0.8307 (ttmm) cc_final: 0.8053 (ttmm)
REVERT: A   69 TRP cc_start: 0.7939 (t-100) cc_final: 0.7626 (t-100)
REVERT: A  117 ASN cc_start: 0.8059 (m-40) cc_final: 0.7760 (m110)
REVERT: A  166 GLU cc_start: 0.7353 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: A  309 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7507 (mmtt)
REVERT: A  329 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7271 (tm-30)
REVERT: A  385 TYR cc_start: 0.7926 (p90) cc_final: 0.7585 (p90)
REVERT: A  441 LYS cc_start: 0.7861 (tttt) cc_final: 0.7622 (ttpp)
REVERT: A  474 MET cc_start: 0.5064 (mmm) cc_final: 0.4742 (mmm)
REVERT: A  477 TRP cc_start: 0.6989 (t-100) cc_final: 0.6515 (t-100)
REVERT: A  483 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7062 (tp30)
REVERT: B  443 SER cc_start: 0.7859 (m) cc_final: 0.7606 (m)
REVERT: B  449 TYR cc_start: 0.7321 (m-80) cc_final: 0.6754 (m-80)
REVERT: B  497 PHE cc_start: 0.7171 (m-80) cc_final: 0.6763 (m-80)
  outliers start: 11
  outliers final: 3
  residues processed: 199
  average time/residue: 0.9570
  time to fit residues: 202.3376
Evaluate side-chains
  176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 173
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0770
   chunk 67 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0050
   chunk 76 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0070
   chunk 2 optimal weight:    0.0980
   chunk 26 optimal weight:    0.9980
   chunk 43 optimal weight:    0.1980
   overall best weight:    0.0770

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 343 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.167626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.148421 restraints weight = 15637.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.97
r_work: 0.3872 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3874
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3874 r_free = 0.3874    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6712  Z= 0.173
  Angle     :  0.631  14.728   9128  Z= 0.316
  Chirality :  0.043   0.202    979
  Planarity :  0.004   0.043   1172
  Dihedral  :  7.162  55.795   1026
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 18.13 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.30), residues: 790
  helix:  1.75 (0.26), residues: 391
  sheet:  1.07 (0.73), residues: 45
  loop : -0.13 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 163 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.015   0.002   PHE B 429 
 TYR   0.027   0.002   TYR A 385 
 ARG   0.006   0.001   ARG A 482 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7923 (m-40) cc_final: 0.7604 (m-40)
REVERT: A   68 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8106 (ttmm)
REVERT: A   69 TRP cc_start: 0.7980 (t-100) cc_final: 0.7650 (t-100)
REVERT: A  117 ASN cc_start: 0.8054 (m-40) cc_final: 0.7765 (m110)
REVERT: A  166 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6874 (tm-30)
REVERT: A  309 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7513 (mmmm)
REVERT: A  329 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7272 (tm-30)
REVERT: A  474 MET cc_start: 0.5106 (mmm) cc_final: 0.4607 (mmm)
REVERT: A  477 TRP cc_start: 0.7028 (t-100) cc_final: 0.6523 (t-100)
REVERT: A  478 TRP cc_start: 0.7490 (m100) cc_final: 0.7239 (m100)
REVERT: A  499 ASP cc_start: 0.7794 (m-30) cc_final: 0.7236 (m-30)
REVERT: B  433 VAL cc_start: 0.7339 (m) cc_final: 0.6925 (p)
  outliers start: 7
  outliers final: 4
  residues processed: 165
  average time/residue: 1.0868
  time to fit residues: 189.8964
Evaluate side-chains
  160 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 156
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  512 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 36 optimal weight:    0.3980
   chunk 59 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0170
   chunk 43 optimal weight:    0.1980
   chunk 31 optimal weight:    0.3980
   chunk 48 optimal weight:    0.0770
   chunk 30 optimal weight:    0.1980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.1576

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
A 493 HIS
B 343 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.166086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.145345 restraints weight = 21264.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 3.58
r_work: 0.3812 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3814
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3814 r_free = 0.3814    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3814
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6712  Z= 0.197
  Angle     :  0.652  14.082   9128  Z= 0.329
  Chirality :  0.044   0.189    979
  Planarity :  0.005   0.041   1172
  Dihedral  :  5.991  57.361   1026
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.71 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.30), residues: 790
  helix:  1.66 (0.26), residues: 389
  sheet:  0.99 (0.73), residues: 45
  loop : -0.18 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 610 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.024   0.002   PHE B 377 
 TYR   0.023   0.002   TYR A 385 
 ARG   0.005   0.001   ARG B 466 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7960 (m-40) cc_final: 0.7677 (m-40)
REVERT: A   68 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8125 (ttmm)
REVERT: A   69 TRP cc_start: 0.8065 (t-100) cc_final: 0.7730 (t-100)
REVERT: A   75 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7698 (mt-10)
REVERT: A  117 ASN cc_start: 0.8101 (m-40) cc_final: 0.7783 (m110)
REVERT: A  131 LYS cc_start: 0.7261 (pttm) cc_final: 0.6820 (pttm)
REVERT: A  166 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6969 (tm-30)
REVERT: A  182 GLU cc_start: 0.7341 (tt0) cc_final: 0.6949 (tp30)
REVERT: A  281 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7468 (mt)
REVERT: A  309 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7608 (mmmm)
REVERT: A  329 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7485 (tm-30)
REVERT: A  457 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7640 (mm-30)
REVERT: A  462 MET cc_start: 0.7169 (mtt) cc_final: 0.6581 (mtm)
REVERT: A  465 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8003 (mptp)
REVERT: A  474 MET cc_start: 0.5197 (mmm) cc_final: 0.4858 (mmm)
REVERT: A  477 TRP cc_start: 0.7081 (t-100) cc_final: 0.6833 (t-100)
REVERT: A  499 ASP cc_start: 0.7912 (m-30) cc_final: 0.7676 (m-30)
REVERT: A  559 ARG cc_start: 0.8377 (ppp80) cc_final: 0.8170 (ptt90)
REVERT: B  433 VAL cc_start: 0.7262 (m) cc_final: 0.6902 (p)
REVERT: B  449 TYR cc_start: 0.7429 (m-80) cc_final: 0.6845 (m-80)
REVERT: B  497 PHE cc_start: 0.6671 (m-10) cc_final: 0.6235 (m-10)
  outliers start: 18
  outliers final: 5
  residues processed: 178
  average time/residue: 1.1306
  time to fit residues: 212.4639
Evaluate side-chains
  174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 167
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 MET
Chi-restraints excluded: chain A residue  181 GLU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  465 LYS
Chi-restraints excluded: chain A residue  597 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 23 optimal weight:    0.0270
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 33 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    0.1980
   chunk 51 optimal weight:    0.4980
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0870
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.2016

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

Flipped N/Q/H residues before XYZ refinement:
** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
B 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.164753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.143671 restraints weight = 26011.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 4.07
r_work: 0.3775 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3776 r_free = 0.3776    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6712  Z= 0.225
  Angle     :  0.660  13.537   9128  Z= 0.335
  Chirality :  0.044   0.182    979
  Planarity :  0.004   0.044   1172
  Dihedral  :  5.733  57.297   1026
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.99 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.30), residues: 790
  helix:  1.54 (0.26), residues: 392
  sheet:  0.64 (0.74), residues: 44
  loop : -0.26 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 610 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.027   0.002   PHE B 377 
 TYR   0.021   0.002   TYR A  50 
 ARG   0.007   0.001   ARG B 466 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7989 (m-40) cc_final: 0.7688 (m-40)
REVERT: A   68 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8210 (ttmm)
REVERT: A   69 TRP cc_start: 0.8100 (t-100) cc_final: 0.7864 (t-100)
REVERT: A   75 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7739 (mt-10)
REVERT: A  117 ASN cc_start: 0.8180 (m-40) cc_final: 0.7887 (m110)
REVERT: A  131 LYS cc_start: 0.7237 (pttm) cc_final: 0.6814 (pttm)
REVERT: A  182 GLU cc_start: 0.7266 (tt0) cc_final: 0.6889 (tp30)
REVERT: A  281 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7505 (mt)
REVERT: A  329 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7563 (tm-30)
REVERT: A  457 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7769 (mm-30)
REVERT: A  474 MET cc_start: 0.5242 (mmm) cc_final: 0.4704 (mmt)
REVERT: A  489 GLU cc_start: 0.6697 (pm20) cc_final: 0.6471 (pp20)
REVERT: A  499 ASP cc_start: 0.7940 (m-30) cc_final: 0.7531 (m-30)
REVERT: B  433 VAL cc_start: 0.7138 (m) cc_final: 0.6806 (p)
REVERT: B  497 PHE cc_start: 0.6745 (m-10) cc_final: 0.6394 (m-10)
  outliers start: 19
  outliers final: 6
  residues processed: 177
  average time/residue: 1.0536
  time to fit residues: 197.2078
Evaluate side-chains
  174 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 167
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 MET
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  332 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain B residue  402 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 17 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0010
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0770
   chunk 29 optimal weight:    0.0970
   chunk 50 optimal weight:    0.0770
   chunk 32 optimal weight:    0.0970
   chunk 35 optimal weight:    0.2980
   chunk 43 optimal weight:    0.0770
   overall best weight:    0.0658

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.166455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.146373 restraints weight = 20842.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 3.51
r_work: 0.3825 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6712  Z= 0.179
  Angle     :  0.669  13.188   9128  Z= 0.337
  Chirality :  0.043   0.175    979
  Planarity :  0.004   0.039   1172
  Dihedral  :  5.649  55.880   1026
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 21.87 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.30), residues: 790
  helix:  1.59 (0.26), residues: 394
  sheet:  0.65 (0.74), residues: 43
  loop : -0.19 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.034   0.002   PHE B 377 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.005   0.001   ARG A 204 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: A   63 ASN cc_start: 0.7935 (m-40) cc_final: 0.7619 (m-40)
REVERT: A   68 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8243 (ttmm)
REVERT: A   69 TRP cc_start: 0.8093 (t-100) cc_final: 0.7849 (t-100)
REVERT: A   75 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7549 (mt-10)
REVERT: A   94 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7743 (ttpp)
REVERT: A  131 LYS cc_start: 0.7201 (pttm) cc_final: 0.6784 (pttm)
REVERT: A  182 GLU cc_start: 0.7026 (tt0) cc_final: 0.6656 (tp30)
REVERT: A  281 LEU cc_start: 0.7712 (tt) cc_final: 0.7500 (mt)
REVERT: A  329 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7503 (tm-30)
REVERT: A  474 MET cc_start: 0.5265 (mmm) cc_final: 0.4422 (mmm)
REVERT: A  499 ASP cc_start: 0.7816 (m-30) cc_final: 0.7451 (m-30)
REVERT: A  600 LYS cc_start: 0.7222 (ptmm) cc_final: 0.6927 (ptmm)
REVERT: B  433 VAL cc_start: 0.7083 (m) cc_final: 0.6800 (p)
REVERT: B  497 PHE cc_start: 0.6623 (m-10) cc_final: 0.6408 (m-10)
  outliers start: 15
  outliers final: 6
  residues processed: 163
  average time/residue: 1.1347
  time to fit residues: 195.1138
Evaluate side-chains
  161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain B residue  446 SER
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 16 optimal weight:    0.2980
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0670
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0170
   chunk 72 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 47 optimal weight:    0.1980
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.2156

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

Flipped N/Q/H residues before XYZ refinement:
A 442 GLN
B 505 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.163922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.144901 restraints weight = 15185.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.91
r_work: 0.3825 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3827 r_free = 0.3827    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.4394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6712  Z= 0.232
  Angle     :  0.694  12.544   9128  Z= 0.352
  Chirality :  0.045   0.186    979
  Planarity :  0.005   0.044   1172
  Dihedral  :  5.777  57.115   1026
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 23.17 %
    Favored  : 75.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 790
  helix:  1.46 (0.26), residues: 393
  sheet:  0.66 (0.74), residues: 43
  loop : -0.36 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 168 
 HIS   0.007   0.001   HIS A 374 
 PHE   0.033   0.002   PHE B 377 
 TYR   0.023   0.002   TYR A  50 
 ARG   0.008   0.001   ARG B 466 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 164
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASN cc_start: 0.7903 (m-40) cc_final: 0.7598 (m-40)
REVERT: A   69 TRP cc_start: 0.8123 (t-100) cc_final: 0.7917 (t-100)
REVERT: A   75 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7443 (mt-10)
REVERT: A  131 LYS cc_start: 0.7174 (pttm) cc_final: 0.6788 (pttm)
REVERT: A  329 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7456 (tm-30)
REVERT: A  474 MET cc_start: 0.5273 (mmm) cc_final: 0.5070 (mmt)
REVERT: A  600 LYS cc_start: 0.7270 (ptmm) cc_final: 0.6883 (ptmm)
REVERT: B  345 THR cc_start: 0.8305 (p) cc_final: 0.8035 (p)
REVERT: B  433 VAL cc_start: 0.7065 (m) cc_final: 0.6816 (p)
  outliers start: 12
  outliers final: 6
  residues processed: 169
  average time/residue: 1.1329
  time to fit residues: 201.9560
Evaluate side-chains
  162 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 156
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.0470
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 58 optimal weight:    0.2980
   chunk 72 optimal weight:    0.3980
   chunk 25 optimal weight:    0.0870
   chunk 34 optimal weight:    0.0030
   overall best weight:    0.0824

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

Flipped N/Q/H residues before XYZ refinement:
B 343 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.165565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.145869 restraints weight = 18885.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 3.35
r_work: 0.3834 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6712  Z= 0.187
  Angle     :  0.709  12.497   9128  Z= 0.353
  Chirality :  0.045   0.389    979
  Planarity :  0.005   0.056   1172
  Dihedral  :  5.657  55.532   1026
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 24.03 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.30), residues: 790
  helix:  1.46 (0.26), residues: 388
  sheet:  0.53 (0.75), residues: 43
  loop : -0.32 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 168 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.029   0.002   PHE B 377 
 TYR   0.019   0.001   TYR A  50 
 ARG   0.009   0.001   ARG B 457 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8090 (t-100) cc_final: 0.7884 (t-100)
REVERT: A  131 LYS cc_start: 0.7115 (pttm) cc_final: 0.6795 (pttm)
REVERT: A  168 TRP cc_start: 0.7754 (t-100) cc_final: 0.7549 (t-100)
REVERT: A  329 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: A  474 MET cc_start: 0.5362 (mmm) cc_final: 0.4714 (mmt)
REVERT: A  499 ASP cc_start: 0.7783 (m-30) cc_final: 0.7433 (m-30)
REVERT: A  595 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7815 (mt)
REVERT: B  342 PHE cc_start: 0.7096 (m-80) cc_final: 0.6814 (m-80)
REVERT: B  345 THR cc_start: 0.8275 (p) cc_final: 0.8035 (p)
REVERT: B  433 VAL cc_start: 0.7133 (m) cc_final: 0.6928 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 159
  average time/residue: 1.1462
  time to fit residues: 192.7618
Evaluate side-chains
  155 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 148
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  206 ASP
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.0670
   chunk 42 optimal weight:    0.1980
   chunk 68 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0040
   chunk 32 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 75 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0770
   overall best weight:    0.1688

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
B 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.164637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.145073 restraints weight = 17402.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 3.20
r_work: 0.3831 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3833 r_free = 0.3833    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6712  Z= 0.217
  Angle     :  0.743  12.215   9128  Z= 0.372
  Chirality :  0.045   0.346    979
  Planarity :  0.005   0.076   1172
  Dihedral  :  5.692  56.106   1026
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 25.47 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.30), residues: 790
  helix:  1.43 (0.27), residues: 387
  sheet:  0.41 (0.74), residues: 43
  loop : -0.40 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.014   0.001   PHE B 429 
 TYR   0.024   0.002   TYR A  41 
 ARG   0.009   0.001   ARG B 457 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8100 (t-100) cc_final: 0.7890 (t-100)
REVERT: A  131 LYS cc_start: 0.7148 (pttm) cc_final: 0.6786 (pttm)
REVERT: A  329 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7560 (tm-30)
REVERT: A  366 MET cc_start: 0.8390 (mtp) cc_final: 0.8088 (mtm)
REVERT: A  474 MET cc_start: 0.5331 (mmm) cc_final: 0.4685 (mmt)
REVERT: A  499 ASP cc_start: 0.7735 (m-30) cc_final: 0.7391 (m-30)
REVERT: A  595 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7820 (mt)
REVERT: A  600 LYS cc_start: 0.7269 (ptmm) cc_final: 0.6979 (ptmm)
REVERT: B  342 PHE cc_start: 0.7082 (m-80) cc_final: 0.6822 (m-80)
REVERT: B  345 THR cc_start: 0.8320 (p) cc_final: 0.8085 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 160
  average time/residue: 1.0462
  time to fit residues: 177.4600
Evaluate side-chains
  159 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 153
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0270
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0010
   chunk 34 optimal weight:    0.0770
   chunk 52 optimal weight:    0.0370
   chunk 73 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0670
   chunk 53 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.0418

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
B 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.167305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.147492 restraints weight = 20982.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 3.55
r_work: 0.3848 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.4827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6712  Z= 0.187
  Angle     :  0.758  12.767   9128  Z= 0.381
  Chirality :  0.044   0.327    979
  Planarity :  0.005   0.073   1172
  Dihedral  :  5.585  55.021   1026
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 26.19 %
    Favored  : 72.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.30), residues: 790
  helix:  1.48 (0.26), residues: 382
  sheet:  0.22 (0.74), residues: 43
  loop : -0.43 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 603 
 TYR   0.020   0.001   TYR A  50 
 ARG   0.010   0.001   ARG B 457 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 153
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 TRP cc_start: 0.8121 (t-100) cc_final: 0.7889 (t-100)
REVERT: A  131 LYS cc_start: 0.7076 (pttm) cc_final: 0.6754 (pttm)
REVERT: A  329 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: A  351 LEU cc_start: 0.7804 (mp) cc_final: 0.7599 (mp)
REVERT: A  366 MET cc_start: 0.8162 (mtp) cc_final: 0.7915 (mtm)
REVERT: A  474 MET cc_start: 0.5399 (mmm) cc_final: 0.5159 (mmt)
REVERT: A  489 GLU cc_start: 0.6718 (pm20) cc_final: 0.6517 (pp20)
REVERT: A  522 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8330 (pt0)
REVERT: A  595 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7850 (mt)
REVERT: B  345 THR cc_start: 0.8292 (p) cc_final: 0.8054 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 158
  average time/residue: 1.1238
  time to fit residues: 187.1356
Evaluate side-chains
  152 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 145
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain B residue  402 ILE
Chi-restraints excluded: chain B residue  437 ASN
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.0970
   chunk 36 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0670
   chunk 68 optimal weight:    0.0980
   chunk 8 optimal weight:    0.2980
   chunk 27 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.1314

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  42 GLN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 437 ASN
B 450 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.164540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.144761 restraints weight = 21371.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 3.54
r_work: 0.3833 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3834 r_free = 0.3834    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.220   6712  Z= 0.382
  Angle     :  1.135  59.165   9128  Z= 0.647
  Chirality :  0.061   1.256    979
  Planarity :  0.006   0.072   1172
  Dihedral  :  5.609  55.030   1026
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 25.47 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.30), residues: 790
  helix:  1.42 (0.26), residues: 388
  sheet:  0.25 (0.76), residues: 42
  loop : -0.42 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 603 
 TYR   0.021   0.002   TYR A 183 
 ARG   0.007   0.001   ARG B 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6372.70 seconds
wall clock time: 115 minutes 26.45 seconds (6926.45 seconds total)