Starting phenix.real_space_refine
on Sun Aug  4 13:26:23 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_38495.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_38495.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_38495.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_38495.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xn2_38495/08_2024/8xn2_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
    Residue "A PHE  315": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  497": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.76, per 1000 atoms: 1.34
  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  - 3.50
        Amino acid           : False - 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: 2.67
  Conformation dependent library (CDL) restraints added in 1.8 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: 0.66
  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: 1.76

  Time building geometry restraints manager: 2.93 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:
       99.05 -   106.04: 165
      106.04 -   113.03: 3570
      113.03 -   120.02: 2332
      120.02 -   127.01: 2953
      127.01 -   134.00: 108
  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:             17.830
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     28.160
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.360
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.762 
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: 0.9837
  time to fit residues: 237.2916
Evaluate side-chains
  178 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
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 fitting.
    rotamer outliers: 11
    poor density    : 196
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7242 (tm-30) cc_final: 0.7009 (tm-30)
REVERT: A   42 GLN cc_start: 0.7343 (mt0) cc_final: 0.7051 (mt0)
REVERT: A   63 ASN cc_start: 0.7294 (m-40) cc_final: 0.7013 (m-40)
REVERT: A   68 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7733 (ttmm)
REVERT: A   69 TRP cc_start: 0.7401 (t-100) cc_final: 0.6980 (t-100)
REVERT: A   79 LEU cc_start: 0.7850 (mt) cc_final: 0.7626 (tt)
REVERT: A  156 LEU cc_start: 0.7150 (tt) cc_final: 0.6903 (tm)
REVERT: A  166 GLU cc_start: 0.6748 (tm-30) cc_final: 0.6477 (tm-30)
REVERT: A  171 GLU cc_start: 0.6220 (tp30) cc_final: 0.5900 (tm-30)
REVERT: A  247 LYS cc_start: 0.6756 (tppt) cc_final: 0.6496 (tppt)
REVERT: A  249 MET cc_start: 0.7037 (ttm) cc_final: 0.6545 (tmt)
REVERT: A  309 LYS cc_start: 0.6824 (mmtt) cc_final: 0.6504 (mmtt)
REVERT: A  310 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7120 (mt-10)
REVERT: A  315 PHE cc_start: 0.7797 (m-80) cc_final: 0.7495 (m-80)
REVERT: A  320 LEU cc_start: 0.7638 (mt) cc_final: 0.7382 (mm)
REVERT: A  324 THR cc_start: 0.7046 (m) cc_final: 0.6836 (p)
REVERT: A  329 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6412 (tm-30)
REVERT: A  332 MET cc_start: 0.7184 (ptm) cc_final: 0.6846 (ttm)
REVERT: A  349 TRP cc_start: 0.7667 (m100) cc_final: 0.7262 (m100)
REVERT: A  382 ASP cc_start: 0.7006 (m-30) cc_final: 0.6800 (m-30)
REVERT: A  385 TYR cc_start: 0.7170 (p90) cc_final: 0.6912 (p90)
REVERT: A  408 MET cc_start: 0.7075 (mmt) cc_final: 0.6832 (mmt)
REVERT: A  441 LYS cc_start: 0.6497 (tttt) cc_final: 0.6054 (ttpp)
REVERT: A  465 LYS cc_start: 0.7949 (mttp) cc_final: 0.7597 (mttp)
REVERT: A  467 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6658 (mt-10)
REVERT: A  474 MET cc_start: 0.4134 (mmm) cc_final: 0.3422 (mmm)
REVERT: A  477 TRP cc_start: 0.5393 (t-100) cc_final: 0.4626 (t-100)
REVERT: A  482 ARG cc_start: 0.6486 (ttm170) cc_final: 0.6087 (ttm-80)
REVERT: A  483 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6575 (tp30)
REVERT: A  489 GLU cc_start: 0.6202 (pm20) cc_final: 0.5803 (pm20)
REVERT: A  559 ARG cc_start: 0.7560 (ptm-80) cc_final: 0.7282 (ppp80)
REVERT: A  564 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7166 (mm-30)
REVERT: A  572 ASN cc_start: 0.7338 (t0) cc_final: 0.7046 (t0)
REVERT: A  577 LYS cc_start: 0.7705 (mttp) cc_final: 0.7482 (mtmm)
REVERT: A  582 ARG cc_start: 0.7114 (tpp80) cc_final: 0.6865 (mmp-170)
REVERT: A  603 PHE cc_start: 0.6402 (t80) cc_final: 0.5892 (t80)
REVERT: A  611 SER cc_start: 0.7212 (m) cc_final: 0.6883 (p)
REVERT: B  377 PHE cc_start: 0.7839 (t80) cc_final: 0.7588 (t80)
REVERT: B  414 GLN cc_start: 0.7567 (mm110) cc_final: 0.7246 (mm110)
REVERT: B  449 TYR cc_start: 0.7129 (m-80) cc_final: 0.6218 (m-80)
REVERT: B  452 LEU cc_start: 0.7682 (mt) cc_final: 0.7260 (mm)
REVERT: B  497 PHE cc_start: 0.6693 (m-80) cc_final: 0.5698 (m-80)
  outliers start: 11
  outliers final: 3
  residues processed: 199
  average time/residue: 0.9248
  time to fit residues: 195.5815
Evaluate side-chains
  182 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 179
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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 39 optimal weight:    0.2980
   chunk 21 optimal weight:    0.3980
   chunk 58 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0020
   chunk 70 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0570
   chunk 63 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0970
   chunk 56 optimal weight:    0.0970
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.0902

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6147
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6712  Z= 0.166
  Angle     :  0.583   9.472   9128  Z= 0.296
  Chirality :  0.042   0.200    979
  Planarity :  0.004   0.043   1172
  Dihedral  :  6.950  56.048   1026
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 17.27 %
    Favored  : 81.58 %
  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:  1.75 (0.26), residues: 391
  sheet:  0.92 (0.73), residues: 49
  loop : -0.08 (0.34), residues: 350

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   0.017   0.001   PHE B 429 
 TYR   0.024   0.002   TYR A 385 
 ARG   0.004   0.000   ARG A 518 

*********************** 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
  187 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 179
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6849 (tm-30)
REVERT: A   42 GLN cc_start: 0.7340 (mt0) cc_final: 0.7059 (mt0)
REVERT: A   62 MET cc_start: 0.7014 (ttm) cc_final: 0.6762 (ttp)
REVERT: A   63 ASN cc_start: 0.7374 (m-40) cc_final: 0.6986 (m-40)
REVERT: A   68 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7780 (ttmm)
REVERT: A   69 TRP cc_start: 0.7444 (t-100) cc_final: 0.7045 (t-100)
REVERT: A   76 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7738 (mm-40)
REVERT: A   79 LEU cc_start: 0.7868 (mt) cc_final: 0.7593 (tt)
REVERT: A  156 LEU cc_start: 0.7060 (tt) cc_final: 0.6857 (tm)
REVERT: A  166 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6373 (tm-30)
REVERT: A  171 GLU cc_start: 0.6193 (tp30) cc_final: 0.5990 (tm-30)
REVERT: A  249 MET cc_start: 0.7022 (ttm) cc_final: 0.6499 (tmm)
REVERT: A  309 LYS cc_start: 0.6934 (mmtt) cc_final: 0.6713 (mmtt)
REVERT: A  310 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7208 (mt-10)
REVERT: A  315 PHE cc_start: 0.7827 (m-80) cc_final: 0.7464 (m-80)
REVERT: A  320 LEU cc_start: 0.7603 (mt) cc_final: 0.7357 (mm)
REVERT: A  324 THR cc_start: 0.7136 (m) cc_final: 0.6926 (p)
REVERT: A  329 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6299 (tm-30)
REVERT: A  349 TRP cc_start: 0.7676 (m100) cc_final: 0.7248 (m100)
REVERT: A  408 MET cc_start: 0.7164 (mmt) cc_final: 0.6929 (mmt)
REVERT: A  441 LYS cc_start: 0.6518 (tttt) cc_final: 0.6072 (ttpp)
REVERT: A  465 LYS cc_start: 0.7906 (mttp) cc_final: 0.7488 (mttm)
REVERT: A  467 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6622 (mt-10)
REVERT: A  474 MET cc_start: 0.3996 (mmm) cc_final: 0.3406 (mmt)
REVERT: A  477 TRP cc_start: 0.5426 (t-100) cc_final: 0.4709 (t-100)
REVERT: A  478 TRP cc_start: 0.5849 (m100) cc_final: 0.5505 (m100)
REVERT: A  482 ARG cc_start: 0.6634 (ttm170) cc_final: 0.5995 (ttp-170)
REVERT: A  489 GLU cc_start: 0.6148 (pm20) cc_final: 0.5737 (pm20)
REVERT: A  499 ASP cc_start: 0.7787 (m-30) cc_final: 0.7370 (m-30)
REVERT: A  559 ARG cc_start: 0.7540 (ptm-80) cc_final: 0.7327 (ppp80)
REVERT: A  564 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7111 (mm-30)
REVERT: A  582 ARG cc_start: 0.7086 (tpp80) cc_final: 0.6851 (mmp-170)
REVERT: A  603 PHE cc_start: 0.6443 (t80) cc_final: 0.5980 (t80)
REVERT: A  611 SER cc_start: 0.7262 (m) cc_final: 0.6927 (p)
REVERT: B  377 PHE cc_start: 0.8074 (t80) cc_final: 0.7829 (t80)
REVERT: B  414 GLN cc_start: 0.7520 (mm110) cc_final: 0.7181 (mm110)
REVERT: B  424 LYS cc_start: 0.7247 (tttt) cc_final: 0.6819 (ttpt)
REVERT: B  433 VAL cc_start: 0.7245 (m) cc_final: 0.6765 (p)
REVERT: B  452 LEU cc_start: 0.7682 (mt) cc_final: 0.7261 (mm)
REVERT: B  468 ILE cc_start: 0.7714 (pt) cc_final: 0.7321 (mt)
REVERT: B  497 PHE cc_start: 0.6772 (m-80) cc_final: 0.6446 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 184
  average time/residue: 1.0912
  time to fit residues: 212.1020
Evaluate side-chains
  175 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 170
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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  496 THR
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 36 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0770
   chunk 33 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 75 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 20 optimal weight:    0.3980
   chunk 62 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
A 117 ASN
A 210 ASN
A 493 HIS
A 524 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6712  Z= 0.304
  Angle     :  0.653   8.026   9128  Z= 0.338
  Chirality :  0.046   0.194    979
  Planarity :  0.005   0.045   1172
  Dihedral  :  6.223  59.724   1026
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.55 %
    Favored  : 80.29 %
  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:  0.87 (0.29), residues: 790
  helix:  1.36 (0.26), residues: 388
  sheet:  0.92 (0.74), residues: 44
  loop : -0.28 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 610 
 HIS   0.009   0.002   HIS A 374 
 PHE   0.018   0.002   PHE A 369 
 TYR   0.022   0.002   TYR A 385 
 ARG   0.008   0.001   ARG A 514 

*********************** 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
  195 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7453 (mt0) cc_final: 0.7086 (mp-120)
REVERT: A   63 ASN cc_start: 0.7443 (m-40) cc_final: 0.7036 (m-40)
REVERT: A   68 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7868 (ttmm)
REVERT: A   69 TRP cc_start: 0.7523 (t-100) cc_final: 0.7298 (t-100)
REVERT: A   79 LEU cc_start: 0.7840 (mt) cc_final: 0.7578 (tt)
REVERT: A  131 LYS cc_start: 0.6708 (pttm) cc_final: 0.6217 (pttm)
REVERT: A  166 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6435 (tm-30)
REVERT: A  182 GLU cc_start: 0.7333 (tt0) cc_final: 0.6800 (mm-30)
REVERT: A  216 ASP cc_start: 0.7391 (p0) cc_final: 0.7105 (p0)
REVERT: A  249 MET cc_start: 0.7215 (ttm) cc_final: 0.6511 (tmm)
REVERT: A  291 ILE cc_start: 0.7564 (tp) cc_final: 0.7192 (mt)
REVERT: A  310 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7273 (mt-10)
REVERT: A  320 LEU cc_start: 0.7697 (mt) cc_final: 0.7427 (mm)
REVERT: A  329 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6423 (tm-30)
REVERT: A  350 ASP cc_start: 0.7053 (t70) cc_final: 0.6840 (t0)
REVERT: A  371 THR cc_start: 0.7289 (m) cc_final: 0.7033 (p)
REVERT: A  385 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6978 (p90)
REVERT: A  441 LYS cc_start: 0.6603 (tttt) cc_final: 0.6151 (ttpp)
REVERT: A  465 LYS cc_start: 0.7959 (mttp) cc_final: 0.7444 (mttm)
REVERT: A  467 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6561 (mt-10)
REVERT: A  474 MET cc_start: 0.3706 (mmm) cc_final: 0.2742 (mmt)
REVERT: A  482 ARG cc_start: 0.6623 (ttm170) cc_final: 0.6331 (ttm-80)
REVERT: A  489 GLU cc_start: 0.6179 (pm20) cc_final: 0.5417 (pm20)
REVERT: A  499 ASP cc_start: 0.7721 (m-30) cc_final: 0.6958 (m-30)
REVERT: A  564 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7184 (mm-30)
REVERT: A  595 LEU cc_start: 0.7324 (mt) cc_final: 0.7118 (mm)
REVERT: A  603 PHE cc_start: 0.6491 (t80) cc_final: 0.6210 (t80)
REVERT: A  611 SER cc_start: 0.7189 (m) cc_final: 0.6783 (p)
REVERT: B  374 PHE cc_start: 0.6981 (m-80) cc_final: 0.6767 (m-10)
REVERT: B  412 PRO cc_start: 0.8128 (Cg_exo) cc_final: 0.7411 (Cg_endo)
REVERT: B  414 GLN cc_start: 0.7490 (mm110) cc_final: 0.7181 (mm110)
REVERT: B  424 LYS cc_start: 0.7407 (tttt) cc_final: 0.7020 (ttpt)
REVERT: B  433 VAL cc_start: 0.7050 (m) cc_final: 0.6637 (p)
REVERT: B  449 TYR cc_start: 0.6985 (m-80) cc_final: 0.6263 (m-80)
REVERT: B  452 LEU cc_start: 0.7813 (mt) cc_final: 0.7379 (mm)
REVERT: B  465 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6558 (mt-10)
REVERT: B  468 ILE cc_start: 0.7750 (pt) cc_final: 0.7420 (mt)
REVERT: B  497 PHE cc_start: 0.7303 (m-80) cc_final: 0.6885 (m-80)
  outliers start: 15
  outliers final: 4
  residues processed: 189
  average time/residue: 0.9797
  time to fit residues: 196.0265
Evaluate side-chains
  183 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 178
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  385 TYR
Chi-restraints excluded: chain A residue  425 SER
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 1 optimal weight:    0.2980
   chunk 56 optimal weight:    0.1980
   chunk 31 optimal weight:    0.3980
   chunk 64 optimal weight:    0.0170
   chunk 52 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9990
   chunk 38 optimal weight:    0.1980
   chunk 67 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 25 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.2018

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

Flipped N/Q/H residues before XYZ refinement:
A 397 ASN
A 493 HIS
B 437 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6251
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6712  Z= 0.219
  Angle     :  0.611   9.593   9128  Z= 0.314
  Chirality :  0.044   0.196    979
  Planarity :  0.004   0.040   1172
  Dihedral  :  5.880  56.709   1026
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.28 %
    Favored  : 78.85 %
  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:  0.93 (0.29), residues: 790
  helix:  1.41 (0.26), residues: 397
  sheet:  0.81 (0.73), residues: 43
  loop : -0.26 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 610 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.019   0.001   PHE B 377 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.006   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
  187 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7460 (mt0) cc_final: 0.7083 (mp-120)
REVERT: A   68 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7855 (ttmm)
REVERT: A   69 TRP cc_start: 0.7511 (t-100) cc_final: 0.7297 (t-100)
REVERT: A   79 LEU cc_start: 0.7812 (mt) cc_final: 0.7545 (tt)
REVERT: A  131 LYS cc_start: 0.6642 (pttm) cc_final: 0.6119 (pttm)
REVERT: A  166 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6448 (tm-30)
REVERT: A  171 GLU cc_start: 0.6119 (tm-30) cc_final: 0.5689 (pp20)
REVERT: A  181 GLU cc_start: 0.6936 (pp20) cc_final: 0.6695 (pp20)
REVERT: A  182 GLU cc_start: 0.7368 (tt0) cc_final: 0.6813 (mm-30)
REVERT: A  249 MET cc_start: 0.7192 (ttm) cc_final: 0.6536 (tmm)
REVERT: A  291 ILE cc_start: 0.7538 (tp) cc_final: 0.7258 (mt)
REVERT: A  310 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7278 (mt-10)
REVERT: A  320 LEU cc_start: 0.7757 (mt) cc_final: 0.7506 (mm)
REVERT: A  325 GLN cc_start: 0.6746 (tp40) cc_final: 0.6164 (tp40)
REVERT: A  329 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6395 (tm-30)
REVERT: A  347 THR cc_start: 0.7185 (m) cc_final: 0.6671 (p)
REVERT: A  350 ASP cc_start: 0.7052 (t70) cc_final: 0.6847 (t0)
REVERT: A  380 GLN cc_start: 0.7327 (mm-40) cc_final: 0.7078 (mm-40)
REVERT: A  441 LYS cc_start: 0.6565 (tttt) cc_final: 0.6124 (ttpp)
REVERT: A  465 LYS cc_start: 0.7946 (mttp) cc_final: 0.7422 (mttm)
REVERT: A  467 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6578 (mt-10)
REVERT: A  474 MET cc_start: 0.3624 (mmm) cc_final: 0.2800 (mmt)
REVERT: A  482 ARG cc_start: 0.6753 (ttm170) cc_final: 0.6123 (ttm-80)
REVERT: A  489 GLU cc_start: 0.6143 (pm20) cc_final: 0.5629 (pm20)
REVERT: A  499 ASP cc_start: 0.7677 (m-30) cc_final: 0.7103 (m-30)
REVERT: A  564 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7173 (mm-30)
REVERT: A  595 LEU cc_start: 0.7309 (mt) cc_final: 0.7089 (mm)
REVERT: A  603 PHE cc_start: 0.6489 (t80) cc_final: 0.6253 (t80)
REVERT: A  611 SER cc_start: 0.7280 (m) cc_final: 0.6863 (p)
REVERT: B  407 VAL cc_start: 0.8155 (t) cc_final: 0.7691 (m)
REVERT: B  414 GLN cc_start: 0.7529 (mm110) cc_final: 0.7202 (mm110)
REVERT: B  424 LYS cc_start: 0.7384 (tttt) cc_final: 0.6994 (ttpt)
REVERT: B  433 VAL cc_start: 0.6999 (m) cc_final: 0.6630 (p)
REVERT: B  449 TYR cc_start: 0.7010 (m-80) cc_final: 0.6311 (m-80)
REVERT: B  452 LEU cc_start: 0.7696 (mt) cc_final: 0.7299 (mm)
REVERT: B  457 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6593 (ttt90)
REVERT: B  468 ILE cc_start: 0.7749 (pt) cc_final: 0.7409 (mt)
REVERT: B  497 PHE cc_start: 0.7202 (m-80) cc_final: 0.6878 (m-80)
  outliers start: 13
  outliers final: 4
  residues processed: 182
  average time/residue: 1.0307
  time to fit residues: 198.5390
Evaluate side-chains
  174 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 170
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 ASP
Chi-restraints excluded: chain B residue  446 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0970
   chunk 75 optimal weight:    0.2980
   chunk 62 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0070
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    0.2980
   chunk 39 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0270
   chunk 8 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   overall best weight:    0.0832

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6231
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6712  Z= 0.173
  Angle     :  0.613  10.622   9128  Z= 0.310
  Chirality :  0.043   0.190    979
  Planarity :  0.004   0.039   1172
  Dihedral  :  5.707  56.220   1026
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 21.58 %
    Favored  : 77.27 %
  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:  1.09 (0.30), residues: 790
  helix:  1.58 (0.26), residues: 400
  sheet:  0.65 (0.71), residues: 43
  loop : -0.22 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.016   0.001   PHE B 374 
 TYR   0.018   0.002   TYR A 385 
 ARG   0.009   0.001   ARG B 466 

*********************** 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
  187 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 179
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7449 (mt0) cc_final: 0.7064 (mp-120)
REVERT: A   68 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7840 (ttmm)
REVERT: A   69 TRP cc_start: 0.7513 (t-100) cc_final: 0.7266 (t-100)
REVERT: A   79 LEU cc_start: 0.7819 (mt) cc_final: 0.7532 (tt)
REVERT: A  131 LYS cc_start: 0.6617 (pttm) cc_final: 0.6109 (pttm)
REVERT: A  166 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6452 (tm-30)
REVERT: A  171 GLU cc_start: 0.6155 (tm-30) cc_final: 0.5756 (pp20)
REVERT: A  192 ARG cc_start: 0.7340 (mtt-85) cc_final: 0.7133 (mtt-85)
REVERT: A  249 MET cc_start: 0.7159 (ttm) cc_final: 0.6521 (tmm)
REVERT: A  310 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7271 (mt-10)
REVERT: A  320 LEU cc_start: 0.7758 (mt) cc_final: 0.7523 (mp)
REVERT: A  325 GLN cc_start: 0.6756 (tp40) cc_final: 0.6153 (tp40)
REVERT: A  329 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6365 (tm-30)
REVERT: A  347 THR cc_start: 0.7114 (m) cc_final: 0.6635 (p)
REVERT: A  441 LYS cc_start: 0.6527 (tttt) cc_final: 0.6093 (ttpp)
REVERT: A  465 LYS cc_start: 0.7949 (mttp) cc_final: 0.7443 (mttm)
REVERT: A  467 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6569 (mt-10)
REVERT: A  474 MET cc_start: 0.3677 (mmm) cc_final: 0.3053 (mmm)
REVERT: A  482 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6344 (ttm-80)
REVERT: A  489 GLU cc_start: 0.6109 (pm20) cc_final: 0.5563 (pm20)
REVERT: A  564 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: A  595 LEU cc_start: 0.7299 (mt) cc_final: 0.7073 (mm)
REVERT: A  611 SER cc_start: 0.7291 (m) cc_final: 0.7001 (p)
REVERT: B  342 PHE cc_start: 0.6622 (m-80) cc_final: 0.6373 (m-80)
REVERT: B  414 GLN cc_start: 0.7547 (mm110) cc_final: 0.7206 (mm110)
REVERT: B  424 LYS cc_start: 0.7332 (tttt) cc_final: 0.6959 (ttpt)
REVERT: B  433 VAL cc_start: 0.6883 (m) cc_final: 0.6591 (p)
REVERT: B  449 TYR cc_start: 0.6994 (m-80) cc_final: 0.6290 (m-80)
REVERT: B  457 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6558 (ttt90)
REVERT: B  462 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6820 (mppt)
REVERT: B  468 ILE cc_start: 0.7736 (pt) cc_final: 0.7398 (mt)
REVERT: B  497 PHE cc_start: 0.7125 (m-80) cc_final: 0.6908 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 183
  average time/residue: 1.0048
  time to fit residues: 194.9629
Evaluate side-chains
  179 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 175
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  425 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0030
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0870
   chunk 30 optimal weight:    0.0980
   chunk 44 optimal weight:    0.0050
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.0982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6712  Z= 0.174
  Angle     :  0.610  11.348   9128  Z= 0.308
  Chirality :  0.042   0.192    979
  Planarity :  0.004   0.038   1172
  Dihedral  :  5.599  56.847   1026
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 21.73 %
    Favored  : 77.27 %
  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:  1.08 (0.30), residues: 790
  helix:  1.60 (0.26), residues: 395
  sheet:  0.59 (0.70), residues: 43
  loop : -0.21 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.021   0.001   PHE B 377 
 TYR   0.021   0.002   TYR A 385 
 ARG   0.010   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
  184 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7447 (mt0) cc_final: 0.7140 (mt0)
REVERT: A   63 ASN cc_start: 0.7172 (m-40) cc_final: 0.6966 (m-40)
REVERT: A   68 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7841 (ttmm)
REVERT: A   69 TRP cc_start: 0.7524 (t-100) cc_final: 0.7239 (t-100)
REVERT: A   79 LEU cc_start: 0.7793 (mt) cc_final: 0.7527 (tt)
REVERT: A  131 LYS cc_start: 0.6506 (pttm) cc_final: 0.6078 (pttm)
REVERT: A  168 TRP cc_start: 0.6381 (t-100) cc_final: 0.6148 (t-100)
REVERT: A  192 ARG cc_start: 0.7341 (mtt-85) cc_final: 0.7119 (mpp-170)
REVERT: A  249 MET cc_start: 0.7145 (ttm) cc_final: 0.6498 (tmm)
REVERT: A  310 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7267 (mt-10)
REVERT: A  312 GLU cc_start: 0.7814 (tt0) cc_final: 0.7612 (tt0)
REVERT: A  320 LEU cc_start: 0.7775 (mt) cc_final: 0.7480 (mm)
REVERT: A  325 GLN cc_start: 0.6821 (tp40) cc_final: 0.6203 (tp40)
REVERT: A  329 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6324 (tm-30)
REVERT: A  347 THR cc_start: 0.7119 (m) cc_final: 0.6771 (p)
REVERT: A  353 LYS cc_start: 0.8293 (mttp) cc_final: 0.7998 (mtpp)
REVERT: A  441 LYS cc_start: 0.6550 (tttt) cc_final: 0.6112 (ttpp)
REVERT: A  465 LYS cc_start: 0.7943 (mttp) cc_final: 0.7446 (mttm)
REVERT: A  467 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6537 (mt-10)
REVERT: A  474 MET cc_start: 0.3712 (mmm) cc_final: 0.2784 (mmt)
REVERT: A  482 ARG cc_start: 0.6768 (ttm170) cc_final: 0.6361 (mtm-85)
REVERT: A  489 GLU cc_start: 0.6054 (pm20) cc_final: 0.5533 (pm20)
REVERT: A  499 ASP cc_start: 0.7585 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  527 GLU cc_start: 0.7104 (tp30) cc_final: 0.6719 (tp30)
REVERT: A  564 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7158 (mm-30)
REVERT: A  571 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6597 (tm-30)
REVERT: A  595 LEU cc_start: 0.7270 (mt) cc_final: 0.7055 (mm)
REVERT: A  611 SER cc_start: 0.7323 (m) cc_final: 0.7038 (p)
REVERT: B  414 GLN cc_start: 0.7547 (mm110) cc_final: 0.7180 (mm110)
REVERT: B  424 LYS cc_start: 0.7316 (tttt) cc_final: 0.6928 (ttpt)
REVERT: B  433 VAL cc_start: 0.6830 (m) cc_final: 0.6528 (p)
REVERT: B  449 TYR cc_start: 0.7040 (m-80) cc_final: 0.6248 (m-80)
REVERT: B  457 ARG cc_start: 0.6970 (mtp85) cc_final: 0.6576 (ttt90)
REVERT: B  462 LYS cc_start: 0.7427 (mmmt) cc_final: 0.6784 (mppt)
REVERT: B  468 ILE cc_start: 0.7727 (pt) cc_final: 0.7392 (mt)
REVERT: B  497 PHE cc_start: 0.7113 (m-80) cc_final: 0.6876 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 180
  average time/residue: 1.0800
  time to fit residues: 204.8777
Evaluate side-chains
  178 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 173
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  597 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0870
   chunk 37 optimal weight:    0.0870
   chunk 7 optimal weight:    0.1980
   chunk 59 optimal weight:    0.0870
   chunk 68 optimal weight:    0.4980
   chunk 72 optimal weight:    0.2980
   chunk 65 optimal weight:    0.1980
   chunk 70 optimal weight:    0.0030
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.0924

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
moved from start:          0.4421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6712  Z= 0.174
  Angle     :  0.617  11.503   9128  Z= 0.313
  Chirality :  0.042   0.192    979
  Planarity :  0.004   0.038   1172
  Dihedral  :  5.558  56.256   1026
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 22.88 %
    Favored  : 76.12 %
  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:  1.07 (0.30), residues: 790
  helix:  1.61 (0.27), residues: 390
  sheet:  0.59 (0.70), residues: 43
  loop : -0.24 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.018   0.001   PHE B 429 
 TYR   0.021   0.001   TYR A 385 
 ARG   0.007   0.001   ARG A 177 

*********************** 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
  182 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 175
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   42 GLN cc_start: 0.7445 (mt0) cc_final: 0.7183 (mt0)
REVERT: A   68 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7839 (ttmm)
REVERT: A   69 TRP cc_start: 0.7534 (t-100) cc_final: 0.7258 (t-100)
REVERT: A   79 LEU cc_start: 0.7768 (mt) cc_final: 0.7522 (tt)
REVERT: A  131 LYS cc_start: 0.6538 (pttm) cc_final: 0.6034 (pttm)
REVERT: A  168 TRP cc_start: 0.6342 (t-100) cc_final: 0.5625 (t-100)
REVERT: A  171 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5734 (pp20)
REVERT: A  192 ARG cc_start: 0.7334 (mtt-85) cc_final: 0.7110 (mpp-170)
REVERT: A  208 GLU cc_start: 0.7455 (tt0) cc_final: 0.7040 (tt0)
REVERT: A  216 ASP cc_start: 0.7444 (p0) cc_final: 0.7186 (p0)
REVERT: A  249 MET cc_start: 0.7139 (ttm) cc_final: 0.6560 (tmm)
REVERT: A  270 MET cc_start: 0.6629 (tpp) cc_final: 0.6380 (ttm)
REVERT: A  310 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7284 (mt-10)
REVERT: A  312 GLU cc_start: 0.7847 (tt0) cc_final: 0.7635 (tt0)
REVERT: A  320 LEU cc_start: 0.7793 (mt) cc_final: 0.7475 (mm)
REVERT: A  329 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6367 (tm-30)
REVERT: A  353 LYS cc_start: 0.8304 (mttp) cc_final: 0.7991 (mtpp)
REVERT: A  441 LYS cc_start: 0.6521 (tttt) cc_final: 0.6084 (ttpp)
REVERT: A  465 LYS cc_start: 0.7923 (mttp) cc_final: 0.7420 (mttm)
REVERT: A  467 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6489 (mt-10)
REVERT: A  474 MET cc_start: 0.3695 (mmm) cc_final: 0.3211 (mmt)
REVERT: A  482 ARG cc_start: 0.6623 (ttm170) cc_final: 0.6208 (mtm-85)
REVERT: A  489 GLU cc_start: 0.5963 (pm20) cc_final: 0.5448 (pm20)
REVERT: A  522 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7141 (pt0)
REVERT: A  527 GLU cc_start: 0.7107 (tp30) cc_final: 0.6718 (tp30)
REVERT: A  564 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7119 (mm-30)
REVERT: A  571 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6622 (tm-30)
REVERT: A  595 LEU cc_start: 0.7271 (mt) cc_final: 0.7061 (mm)
REVERT: A  611 SER cc_start: 0.7350 (m) cc_final: 0.7051 (p)
REVERT: B  342 PHE cc_start: 0.6595 (m-80) cc_final: 0.6177 (m-80)
REVERT: B  414 GLN cc_start: 0.7559 (mm110) cc_final: 0.7180 (mm110)
REVERT: B  424 LYS cc_start: 0.7300 (tttt) cc_final: 0.6936 (ttpt)
REVERT: B  433 VAL cc_start: 0.6821 (m) cc_final: 0.6559 (p)
REVERT: B  449 TYR cc_start: 0.7087 (m-80) cc_final: 0.6347 (m-80)
REVERT: B  457 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6578 (ttt90)
REVERT: B  462 LYS cc_start: 0.7437 (mmmt) cc_final: 0.6795 (mppt)
REVERT: B  468 ILE cc_start: 0.7724 (pt) cc_final: 0.7390 (mt)
REVERT: B  497 PHE cc_start: 0.7108 (m-80) cc_final: 0.6816 (m-80)
  outliers start: 7
  outliers final: 5
  residues processed: 181
  average time/residue: 1.0192
  time to fit residues: 194.8551
Evaluate side-chains
  182 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 176
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  522 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0870
   chunk 51 optimal weight:    0.0170
   overall best weight:    0.1554

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.4569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6712  Z= 0.203
  Angle     :  0.638  11.748   9128  Z= 0.324
  Chirality :  0.043   0.193    979
  Planarity :  0.004   0.038   1172
  Dihedral  :  5.596  56.360   1026
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 23.74 %
    Favored  : 75.40 %
  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:  0.97 (0.30), residues: 790
  helix:  1.51 (0.26), residues: 390
  sheet:  0.58 (0.69), residues: 43
  loop : -0.27 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 168 
 HIS   0.006   0.001   HIS A 374 
 PHE   0.010   0.001   PHE A 588 
 TYR   0.025   0.002   TYR A  50 
 ARG   0.007   0.001   ARG A 559 

*********************** 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
  175 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 169
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7444 (mt0) cc_final: 0.7176 (mt0)
REVERT: A   68 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7883 (ttmm)
REVERT: A   69 TRP cc_start: 0.7540 (t-100) cc_final: 0.7248 (t-100)
REVERT: A   79 LEU cc_start: 0.7743 (mt) cc_final: 0.7506 (tt)
REVERT: A  131 LYS cc_start: 0.6517 (pttm) cc_final: 0.6022 (pttm)
REVERT: A  168 TRP cc_start: 0.6343 (t-100) cc_final: 0.5680 (t-100)
REVERT: A  171 GLU cc_start: 0.6308 (tm-30) cc_final: 0.5870 (pp20)
REVERT: A  192 ARG cc_start: 0.7341 (mtt-85) cc_final: 0.7130 (mtt-85)
REVERT: A  208 GLU cc_start: 0.7467 (tt0) cc_final: 0.6949 (tt0)
REVERT: A  216 ASP cc_start: 0.7476 (p0) cc_final: 0.7230 (p0)
REVERT: A  249 MET cc_start: 0.7170 (ttm) cc_final: 0.6530 (tmm)
REVERT: A  310 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7275 (mt-10)
REVERT: A  312 GLU cc_start: 0.7862 (tt0) cc_final: 0.7642 (tt0)
REVERT: A  320 LEU cc_start: 0.7780 (mt) cc_final: 0.7478 (mm)
REVERT: A  329 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6385 (tm-30)
REVERT: A  353 LYS cc_start: 0.8337 (mttp) cc_final: 0.7972 (mtpp)
REVERT: A  365 THR cc_start: 0.7542 (m) cc_final: 0.7171 (p)
REVERT: A  441 LYS cc_start: 0.6541 (tttt) cc_final: 0.6106 (ttpp)
REVERT: A  465 LYS cc_start: 0.7925 (mttp) cc_final: 0.7431 (mttm)
REVERT: A  467 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6501 (mt-10)
REVERT: A  474 MET cc_start: 0.3718 (mmm) cc_final: 0.2421 (mmt)
REVERT: A  482 ARG cc_start: 0.6560 (ttm170) cc_final: 0.6148 (mtm-85)
REVERT: A  489 GLU cc_start: 0.5993 (pm20) cc_final: 0.5454 (pm20)
REVERT: A  499 ASP cc_start: 0.7600 (m-30) cc_final: 0.7374 (p0)
REVERT: A  522 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (pt0)
REVERT: A  527 GLU cc_start: 0.7103 (tp30) cc_final: 0.6726 (tp30)
REVERT: A  564 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7169 (mm-30)
REVERT: A  571 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6638 (tm-30)
REVERT: A  611 SER cc_start: 0.7319 (m) cc_final: 0.7012 (p)
REVERT: B  342 PHE cc_start: 0.6600 (m-80) cc_final: 0.6134 (m-80)
REVERT: B  407 VAL cc_start: 0.8127 (t) cc_final: 0.7700 (m)
REVERT: B  414 GLN cc_start: 0.7578 (mm110) cc_final: 0.7202 (mm110)
REVERT: B  424 LYS cc_start: 0.7330 (tttt) cc_final: 0.6956 (ttpt)
REVERT: B  433 VAL cc_start: 0.6825 (m) cc_final: 0.6579 (p)
REVERT: B  449 TYR cc_start: 0.7098 (m-80) cc_final: 0.6471 (m-80)
REVERT: B  457 ARG cc_start: 0.6998 (mtp85) cc_final: 0.6603 (ttt90)
REVERT: B  462 LYS cc_start: 0.7445 (mmmt) cc_final: 0.6848 (mppt)
REVERT: B  468 ILE cc_start: 0.7736 (pt) cc_final: 0.7399 (mt)
REVERT: B  497 PHE cc_start: 0.7125 (m-80) cc_final: 0.6804 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 174
  average time/residue: 1.0692
  time to fit residues: 196.2443
Evaluate side-chains
  175 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0370
   chunk 61 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0170
   chunk 47 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   chunk 49 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 57 optimal weight:    0.1980
   chunk 9 optimal weight:    0.0970
   overall best weight:    0.0894

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6219
moved from start:          0.4671

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= 0.182
  Angle     :  0.644  11.700   9128  Z= 0.326
  Chirality :  0.042   0.190    979
  Planarity :  0.004   0.040   1172
  Dihedral  :  5.541  55.498   1026
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 23.17 %
    Favored  : 75.68 %
  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:  0.93 (0.30), residues: 790
  helix:  1.52 (0.26), residues: 389
  sheet:  0.47 (0.70), residues: 43
  loop : -0.33 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 168 
 HIS   0.005   0.001   HIS A 374 
 PHE   0.017   0.001   PHE B 429 
 TYR   0.026   0.002   TYR A  50 
 ARG   0.008   0.001   ARG A 559 

********************** 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
  177 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 169
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7440 (mt0) cc_final: 0.7179 (mt0)
REVERT: A   68 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7870 (ttmm)
REVERT: A   69 TRP cc_start: 0.7547 (t-100) cc_final: 0.7261 (t-100)
REVERT: A   75 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7318 (mt-10)
REVERT: A   79 LEU cc_start: 0.7721 (mt) cc_final: 0.7500 (tt)
REVERT: A  131 LYS cc_start: 0.6530 (pttm) cc_final: 0.6017 (pttm)
REVERT: A  168 TRP cc_start: 0.6255 (t-100) cc_final: 0.5671 (t-100)
REVERT: A  171 GLU cc_start: 0.6327 (tm-30) cc_final: 0.5878 (pp20)
REVERT: A  192 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.7114 (ptp-110)
REVERT: A  208 GLU cc_start: 0.7421 (tt0) cc_final: 0.6992 (tt0)
REVERT: A  216 ASP cc_start: 0.7449 (p0) cc_final: 0.7190 (p0)
REVERT: A  249 MET cc_start: 0.7170 (ttm) cc_final: 0.6515 (tmm)
REVERT: A  310 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7254 (mt-10)
REVERT: A  312 GLU cc_start: 0.7870 (tt0) cc_final: 0.7653 (tt0)
REVERT: A  320 LEU cc_start: 0.7771 (mt) cc_final: 0.7439 (mm)
REVERT: A  329 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6367 (tm-30)
REVERT: A  353 LYS cc_start: 0.8343 (mttp) cc_final: 0.7987 (mtpp)
REVERT: A  375 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6484 (mp0)
REVERT: A  441 LYS cc_start: 0.6521 (tttt) cc_final: 0.6088 (ttpp)
REVERT: A  465 LYS cc_start: 0.7920 (mttp) cc_final: 0.7417 (mttm)
REVERT: A  467 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6484 (mt-10)
REVERT: A  474 MET cc_start: 0.3697 (mmm) cc_final: 0.2627 (mmt)
REVERT: A  482 ARG cc_start: 0.6561 (ttm170) cc_final: 0.6178 (mtm-85)
REVERT: A  489 GLU cc_start: 0.5936 (pm20) cc_final: 0.5338 (pm20)
REVERT: A  499 ASP cc_start: 0.7604 (m-30) cc_final: 0.7386 (p0)
REVERT: A  522 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7158 (pt0)
REVERT: A  527 GLU cc_start: 0.7105 (tp30) cc_final: 0.6772 (tp30)
REVERT: A  564 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7145 (mm-30)
REVERT: A  571 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6612 (tm-30)
REVERT: A  611 SER cc_start: 0.7326 (m) cc_final: 0.7012 (p)
REVERT: B  342 PHE cc_start: 0.6600 (m-80) cc_final: 0.6098 (m-80)
REVERT: B  407 VAL cc_start: 0.8085 (t) cc_final: 0.7676 (m)
REVERT: B  414 GLN cc_start: 0.7578 (mm110) cc_final: 0.7122 (mm110)
REVERT: B  424 LYS cc_start: 0.7317 (tttt) cc_final: 0.6949 (ttpt)
REVERT: B  433 VAL cc_start: 0.6789 (m) cc_final: 0.6552 (p)
REVERT: B  449 TYR cc_start: 0.7124 (m-80) cc_final: 0.6466 (m-80)
REVERT: B  457 ARG cc_start: 0.6955 (mtp85) cc_final: 0.6573 (ttt90)
REVERT: B  462 LYS cc_start: 0.7454 (mmmt) cc_final: 0.6821 (mppt)
REVERT: B  489 TYR cc_start: 0.7150 (m-80) cc_final: 0.6832 (m-80)
REVERT: B  497 PHE cc_start: 0.7128 (m-80) cc_final: 0.6673 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 175
  average time/residue: 1.0852
  time to fit residues: 200.3209
Evaluate side-chains
  176 residues out of total 693 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 169
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  225 ASP
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  425 SER
Chi-restraints excluded: chain A residue  522 GLN
Chi-restraints excluded: chain A residue  597 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0030
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0970
   chunk 54 optimal weight:    0.4980
   chunk 3 optimal weight:    0.0970
   chunk 44 optimal weight:    0.0970
   chunk 70 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.1584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.164439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.144129 restraints weight = 21770.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 3.62
r_work: 0.3789 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6712  Z= 0.209
  Angle     :  0.662  11.852   9128  Z= 0.335
  Chirality :  0.043   0.193    979
  Planarity :  0.005   0.041   1172
  Dihedral  :  5.595  56.122   1026
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 23.45 %
    Favored  : 75.40 %
  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:  0.92 (0.30), residues: 790
  helix:  1.49 (0.26), residues: 389
  sheet:  0.43 (0.70), residues: 43
  loop : -0.29 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 477 
 HIS   0.007   0.001   HIS A 374 
 PHE   0.011   0.001   PHE A 369 
 TYR   0.028   0.002   TYR A  50 
 ARG   0.008   0.001   ARG A 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4128.53 seconds
wall clock time: 72 minutes 32.64 seconds (4352.64 seconds total)