Starting phenix.real_space_refine
on Sat Sep 12 06:37:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6kut_9580/09_2026/6kut_9580.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      27      5.49       5
     S     116      5.16       5
     C    8862      2.51       5
     N    2411      2.21       5
     O    2695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14111
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 688, 5639
          Classifications: {'peptide': 688}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 24, 'TRANS': 663}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 5533
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 696, 5533
          Classifications: {'peptide': 696}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 669}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 2360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2360
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 14, 'TRANS': 280}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "R"
      Number of atoms: 248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 248
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "V"
      Number of atoms: 331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 331
          Classifications: {'RNA': 15}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 3, 'rna3p': 11}
  Time building chain proxies: 3.35, per 1000 atoms: 0.24
  Number of scatterers: 14111
  At special positions: 0
  Unit cell: (115.6, 110.16, 126.48, 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)
     S     116     16.00
     P      27     15.00
     O    2695      8.00
     N    2411      7.00
     C    8862      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 541.4 milliseconds
  

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3176

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 15 sheets defined
      45.9% alpha, 7.7% beta
      6 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 13
    Processing helix  chain 'A' and resid 16 through 27
      removed outlier: 3.520A  pdb=" N   ILE A  20 " --> pdb=" O   ALA A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 49
      removed outlier: 3.919A  pdb=" N   SER A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 149 through 169
      removed outlier: 4.168A  pdb=" N   THR A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A 169 " --> pdb=" O   GLU A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 198
      removed outlier: 3.701A  pdb=" N   ASP A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 217
    Processing helix  chain 'A' and resid 223 through 234
      removed outlier: 3.501A  pdb=" N   ALA A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 295
    Processing helix  chain 'A' and resid 312 through 328
    Processing helix  chain 'A' and resid 336 through 342
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.870A  pdb=" N   GLU A 385 " --> pdb=" O   TRP A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 432
    Processing helix  chain 'A' and resid 434 through 457
      removed outlier: 3.663A  pdb=" N   ARG A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 565
    Processing helix  chain 'A' and resid 569 through 589
      removed outlier: 3.811A  pdb=" N   THR A 573 " --> pdb=" O   CYS A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 637
    Processing helix  chain 'A' and resid 639 through 661
      removed outlier: 3.657A  pdb=" N   GLU A 643 " --> pdb=" O   ASP A 639 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASP A 661 " --> pdb=" O   GLN A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 680
    Processing helix  chain 'A' and resid 684 through 703
      removed outlier: 3.607A  pdb=" N   SER A 703 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 11
      removed outlier: 4.011A  pdb=" N   ASN B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 22
      removed outlier: 3.557A  pdb=" N   TYR B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
      removed outlier: 3.994A  pdb=" N   SER B  39 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 99
    Processing helix  chain 'B' and resid 104 through 116
      removed outlier: 3.618A  pdb=" N   PHE B 108 " --> pdb=" O   GLY B 104 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLU B 116 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 127
    Processing helix  chain 'B' and resid 141 through 157
      removed outlier: 3.558A  pdb=" N   GLN B 157 " --> pdb=" O   ILE B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 178
      removed outlier: 3.637A  pdb=" N   TYR B 168 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 224
      removed outlier: 3.518A  pdb=" N   CYS B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 268
    Processing helix  chain 'B' and resid 281 through 293
      removed outlier: 3.579A  pdb=" N   LYS B 285 " --> pdb=" O   LYS B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 324
      removed outlier: 3.845A  pdb=" N   TYR B 320 " --> pdb=" O   GLN B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 339
      removed outlier: 3.646A  pdb=" N   ASP B 337 " --> pdb=" O   ASN B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 348
    Processing helix  chain 'B' and resid 378 through 382
      removed outlier: 3.618A  pdb=" N   LEU B 381 " --> pdb=" O   ARG B 378 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   MET B 382 " --> pdb=" O   LYS B 379 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 378 through 382'
    Processing helix  chain 'B' and resid 383 through 392
      removed outlier: 3.868A  pdb=" N   THR B 392 " --> pdb=" O   ASP B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 397
    Processing helix  chain 'B' and resid 416 through 425
      removed outlier: 3.596A  pdb=" N   PHE B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 509 through 513
      removed outlier: 3.789A  pdb=" N   ALA B 512 " --> pdb=" O   GLU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 537
      removed outlier: 3.512A  pdb=" N   ALA B 527 " --> pdb=" O   ASP B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 560
    Processing helix  chain 'B' and resid 573 through 580
      removed outlier: 3.617A  pdb=" N   ILE B 577 " --> pdb=" O   ARG B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 590
      removed outlier: 3.900A  pdb=" N   LEU B 590 " --> pdb=" O   LYS B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 595
      removed outlier: 3.570A  pdb=" N   GLY B 595 " --> pdb=" O   ILE B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 605
      removed outlier: 3.783A  pdb=" N   LEU B 605 " --> pdb=" O   ILE B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 614
    Processing helix  chain 'B' and resid 618 through 626
      removed outlier: 3.502A  pdb=" N   PHE B 626 " --> pdb=" O   ARG B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 696
      removed outlier: 3.611A  pdb=" N   LYS B 683 " --> pdb=" O   ALA B 679 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 710 through 728
      removed outlier: 4.473A  pdb=" N   ASN B 728 " --> pdb=" O   THR B 724 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 752
      removed outlier: 3.646A  pdb=" N   TYR B 736 " --> pdb=" O   GLY B 732 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER B 752 " --> pdb=" O   ARG B 748 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 14
    Processing helix  chain 'C' and resid 17 through 24
    Processing helix  chain 'C' and resid 31 through 36
    Processing helix  chain 'C' and resid 46 through 56
    Processing helix  chain 'C' and resid 65 through 72
    Processing helix  chain 'C' and resid 98 through 108
      removed outlier: 3.660A  pdb=" N   ILE C 102 " --> pdb=" O   SER C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 122
      removed outlier: 3.529A  pdb=" N   ILE C 118 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 134
    Processing helix  chain 'C' and resid 164 through 175
      removed outlier: 3.927A  pdb=" N   GLU C 168 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE C 175 " --> pdb=" O   MET C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 197
    Processing helix  chain 'C' and resid 206 through 218
      removed outlier: 3.806A  pdb=" N   PHE C 218 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 243
      removed outlier: 3.892A  pdb=" N   GLY C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 723 through 727
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64
    Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 109
      removed outlier: 5.854A  pdb=" N   GLU A 105 " --> pdb=" O   HIS A 131 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   PHE A 133 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   GLY A 107 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 275 through 276
    Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 352
      removed outlier: 5.382A  pdb=" N   LYS A 350 " --> pdb=" O   GLU B 367 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL B 369 " --> pdb=" O   LYS A 350 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ILE A 352 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 466
    Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 604
    Processing sheet with id=AA7, first strand: chain 'A' and resid 666 through 667
      removed outlier: 3.575A  pdb=" N   PHE A 666 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY B 485 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133
    Processing sheet with id=AB1, first strand: chain 'B' and resid 181 through 185
    Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245
    Processing sheet with id=AB3, first strand: chain 'B' and resid 492 through 493
      removed outlier: 3.734A  pdb=" N   PHE B 493 " --> pdb=" O   MET B 496 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 663 through 664
      removed outlier: 4.622A  pdb=" N   ARG B 663 " --> pdb=" O   MET C  62 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153
    Processing sheet with id=AB6, first strand: chain 'C' and resid 736 through 740

    566 hydrogen bonds defined for protein.
    1584 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      17 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 2.59

  Time building geometry restraints manager: 1.54 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: 4212
        1.34 -     1.46: 2632
        1.46 -     1.58: 7354
        1.58 -     1.70: 52
        1.70 -     1.82: 191
  Bond restraints: 14441
  Sorted by residual:
  bond pdb=" CA  ILE B 730 "
       pdb=" C   ILE B 730 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.27e-02 6.20e+03 9.97e+00
  bond pdb=" C   GLU B 394 "
       pdb=" N   PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.334  1.382 -0.048 2.34e-02 1.83e+03 4.21e+00
  bond pdb=" C   ILE C  73 "
       pdb=" N   PRO C  74 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.30e-02 5.92e+03 3.85e+00
  bond pdb=" C   LEU B 487 "
       pdb=" N   PRO B 488 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.045 2.34e-02 1.83e+03 3.62e+00
  bond pdb=" N1    U R   2 "
       pdb=" C2    U R   2 "
    ideal  model  delta    sigma   weight residual
    1.381  1.396 -0.015 9.00e-03 1.23e+04 2.77e+00
  ... (remaining 14436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 19112
        2.40 -     4.80: 359
        4.80 -     7.20: 46
        7.20 -     9.60: 13
        9.60 -    12.00: 3
  Bond angle restraints: 19533
  Sorted by residual:
  angle pdb=" N   ILE B 250 "
        pdb=" CA  ILE B 250 "
        pdb=" C   ILE B 250 "
      ideal   model   delta    sigma   weight residual
     113.53  107.10    6.43 9.80e-01 1.04e+00 4.30e+01
  angle pdb=" C4'   U R   9 "
        pdb=" C3'   U R   9 "
        pdb=" O3'   U R   9 "
      ideal   model   delta    sigma   weight residual
     109.40  121.40  -12.00 2.10e+00 2.27e-01 3.26e+01
  angle pdb=" O5'   A V   7 "
        pdb=" C5'   A V   7 "
        pdb=" C4'   A V   7 "
      ideal   model   delta    sigma   weight residual
     109.40  112.93   -3.53 8.00e-01 1.56e+00 1.95e+01
  angle pdb=" O4'   A V   7 "
        pdb=" C1'   A V   7 "
        pdb=" N9    A V   7 "
      ideal   model   delta    sigma   weight residual
     108.20  111.49   -3.29 8.00e-01 1.56e+00 1.69e+01
  angle pdb=" O2    U R   2 "
        pdb=" C2    U R   2 "
        pdb=" N3    U R   2 "
      ideal   model   delta    sigma   weight residual
     122.20  119.33    2.87 7.00e-01 2.04e+00 1.68e+01
  ... (remaining 19528 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.93: 8763
       35.93 -    71.87: 105
       71.87 -   107.80: 10
      107.80 -   143.73: 1
      143.73 -   179.66: 1
  Dihedral angle restraints: 8880
    sinusoidal: 3986
      harmonic: 4894
  Sorted by residual:
  dihedral pdb=" CA  LEU C 181 "
           pdb=" C   LEU C 181 "
           pdb=" N   ALA C 182 "
           pdb=" CA  ALA C 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.05   24.95     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" CA  VAL C 740 "
           pdb=" C   VAL C 740 "
           pdb=" N   GLY C 741 "
           pdb=" CA  GLY C 741 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  PHE B 726 "
           pdb=" C   PHE B 726 "
           pdb=" N   GLU B 727 "
           pdb=" CA  GLU B 727 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.03  -23.97     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 8877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.121: 2067
       0.121 -    0.242: 68
       0.242 -    0.362: 5
       0.362 -    0.483: 1
       0.483 -    0.604: 1
  Chirality restraints: 2142
  Sorted by residual:
  chirality pdb=" C3'   U R   9 "
            pdb=" C4'   U R   9 "
            pdb=" O3'   U R   9 "
            pdb=" C2'   U R   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.14   -0.60 2.00e-01 2.50e+01 9.12e+00
  chirality pdb=" CB  ILE C 186 "
            pdb=" CA  ILE C 186 "
            pdb=" CG1 ILE C 186 "
            pdb=" CG2 ILE C 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CB  ILE B 304 "
            pdb=" CA  ILE B 304 "
            pdb=" CG1 ILE B 304 "
            pdb=" CG2 ILE B 304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 2139 not shown)

  Planarity restraints: 2391
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  36 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.51e+00
        pdb=" C   ILE A  36 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ILE A  36 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER A  37 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  35 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.08e+00
        pdb=" C   MET A  35 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   MET A  35 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A  36 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  37 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.69e+00
        pdb=" C   SER A  37 "    0.048 2.00e-02 2.50e+03
        pdb=" O   SER A  37 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A  38 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2388 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 841
        2.73 -     3.27: 13142
        3.27 -     3.82: 21297
        3.82 -     4.36: 26311
        4.36 -     4.90: 44451
  Nonbonded interactions: 106042
  Sorted by model distance:
  nonbonded pdb=" OP2   G V   5 "
            pdb=" N2    G V   5 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" OE1 GLU A 209 "
            pdb=" NH2 ARG A 212 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   THR B 287 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER A 163 "
            pdb=" NH1 ARG A 167 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   GLU C 188 "
            pdb=" OG  SER C 191 "
     model   vdw
     2.291 3.040
  ... (remaining 106037 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.370
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
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      :  0.003   0.052  14441  Z= 0.186
  Angle     :  0.819  11.996  19533  Z= 0.485
  Chirality :  0.054   0.604   2142
  Planarity :  0.006   0.056   2391
  Dihedral  : 11.953 179.664   5704
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.56 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  2.17 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.00 (0.15), residues: 1653
  helix: -3.60 (0.11), residues: 711
  sheet: -1.73 (0.42), residues: 143
  loop : -3.35 (0.18), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 438 
 TYR   0.018   0.002   TYR B  22 
 PHE   0.023   0.002   PHE A 156 
 TRP   0.030   0.002   TRP A 386 
 HIS   0.010   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.19 (14441)
  covalent geometry    : angle       0.81851 /  0.49 (19533)
  hydrogen bonds       : bond        0.14163 /  9.53 (  583)
  hydrogen bonds       : angle       9.82739 /  6.88 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  569 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 559
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7001 (ptp90)
REVERT: A   68 LEU cc_start: 0.4460 (OUTLIER) cc_final: 0.3901 (tt)
REVERT: A  171 MET cc_start: 0.6165 (mtm) cc_final: 0.5772 (mtt)
REVERT: A  340 ASP cc_start: 0.8500 (m-30) cc_final: 0.8149 (m-30)
REVERT: A  350 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7732 (ttpp)
REVERT: A  365 PHE cc_start: 0.6679 (t80) cc_final: 0.6118 (t80)
REVERT: A  427 LEU cc_start: 0.9231 (tt) cc_final: 0.8605 (tt)
REVERT: A  497 MET cc_start: 0.8129 (mpt) cc_final: 0.7254 (mmt)
REVERT: A  511 ASN cc_start: 0.8176 (t0) cc_final: 0.7932 (t0)
REVERT: A  526 VAL cc_start: 0.9302 (t) cc_final: 0.8995 (p)
REVERT: A  561 ASP cc_start: 0.7017 (t70) cc_final: 0.6716 (t70)
REVERT: A  565 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8471 (mtmm)
REVERT: A  619 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8039 (tmtt)
REVERT: A  649 GLN cc_start: 0.8429 (pt0) cc_final: 0.8172 (pt0)
REVERT: B  335 MET cc_start: 0.7270 (ttt) cc_final: 0.6958 (tpp)
REVERT: B  336 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7602 (ttmm)
REVERT: B  341 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7488 (p)
REVERT: B  393 ILE cc_start: 0.9419 (tt) cc_final: 0.8045 (tt)
REVERT: B  415 MET cc_start: 0.6892 (mtt) cc_final: 0.6641 (mtt)
REVERT: B  490 LEU cc_start: 0.8837 (tp) cc_final: 0.8389 (tp)
REVERT: B  574 MET cc_start: 0.6910 (mmm) cc_final: 0.6653 (tpt)
REVERT: B  678 MET cc_start: 0.2875 (mmt) cc_final: 0.2094 (tpp)
REVERT: B  685 TYR cc_start: 0.6774 (m-10) cc_final: 0.6495 (m-80)
REVERT: B  715 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8313 (pp20)
REVERT: C    9 LYS cc_start: 0.7809 (tttm) cc_final: 0.7215 (mttm)
REVERT: C   13 ASN cc_start: 0.7450 (m-40) cc_final: 0.7084 (m-40)
REVERT: C   69 GLU cc_start: 0.7184 (pt0) cc_final: 0.6854 (pp20)
REVERT: C   81 ASP cc_start: 0.7285 (m-30) cc_final: 0.7040 (m-30)
REVERT: C  190 PHE cc_start: 0.6241 (t80) cc_final: 0.5977 (t80)
  outliers start: 10
  outliers final: 0
  residues processed: 565
  average time/residue: 0.1319
  time to fit residues: 105.4005
Evaluate side-chains
  326 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 324
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 ASN
A 170 ASN
A 263 HIS
A 638 ASN
A 670 GLN
B  70 ASN
B 147 GLN
B 154 GLN
B 170 ASN
B 333 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 477 ASN
B 572 HIS
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 217 GLN
C 742 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.160552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.127990 restraints weight = 25334.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.131199 restraints weight = 14448.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.133296 restraints weight = 9764.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.134690 restraints weight = 7456.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135579 restraints weight = 6217.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14441  Z= 0.169
  Angle     :  0.671   9.584  19533  Z= 0.354
  Chirality :  0.044   0.287   2142
  Planarity :  0.005   0.060   2391
  Dihedral  : 12.768 169.864   2227
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.44 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.38 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.17), residues: 1653
  helix: -1.68 (0.16), residues: 727
  sheet: -1.17 (0.47), residues: 130
  loop : -3.12 (0.18), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 241 
 TYR   0.016   0.002   TYR B  47 
 PHE   0.026   0.002   PHE A 161 
 TRP   0.016   0.001   TRP A 386 
 HIS   0.009   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.17 (14441)
  covalent geometry    : angle       0.67123 /  0.35 (19533)
  hydrogen bonds       : bond        0.05119 /  3.28 (  583)
  hydrogen bonds       : angle       6.36949 /  4.50 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  398 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 396
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7201 (ptp90)
REVERT: A  207 ASN cc_start: 0.8183 (m-40) cc_final: 0.7803 (m-40)
REVERT: A  228 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8704 (ttmt)
REVERT: A  365 PHE cc_start: 0.6722 (t80) cc_final: 0.6210 (t80)
REVERT: A  427 LEU cc_start: 0.9225 (tt) cc_final: 0.8648 (tt)
REVERT: A  442 LYS cc_start: 0.9215 (tttt) cc_final: 0.8903 (ttmm)
REVERT: A  497 MET cc_start: 0.8467 (mpp) cc_final: 0.7925 (mmt)
REVERT: A  511 ASN cc_start: 0.8554 (t0) cc_final: 0.8193 (t0)
REVERT: A  516 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: A  561 ASP cc_start: 0.8070 (t70) cc_final: 0.7427 (t70)
REVERT: A  565 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8686 (mtmm)
REVERT: A  603 TRP cc_start: 0.7022 (m-90) cc_final: 0.6751 (m-90)
REVERT: A  619 LYS cc_start: 0.8425 (mmtt) cc_final: 0.7400 (tmtt)
REVERT: A  677 ILE cc_start: 0.8522 (mt) cc_final: 0.8314 (mt)
REVERT: B   85 VAL cc_start: 0.8877 (t) cc_final: 0.8661 (t)
REVERT: B   96 MET cc_start: 0.8151 (mtt) cc_final: 0.7805 (mtt)
REVERT: B  116 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7461 (mp0)
REVERT: B  130 GLN cc_start: 0.8418 (tp40) cc_final: 0.7598 (tp40)
REVERT: B  289 SER cc_start: 0.8909 (m) cc_final: 0.8620 (p)
REVERT: B  301 MET cc_start: 0.8342 (ttm) cc_final: 0.8087 (ttm)
REVERT: B  336 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8151 (ttmm)
REVERT: B  341 VAL cc_start: 0.8149 (p) cc_final: 0.7796 (p)
REVERT: B  378 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7653 (mmm-85)
REVERT: B  382 MET cc_start: 0.7986 (mtp) cc_final: 0.7711 (mmm)
REVERT: B  383 ASN cc_start: 0.8033 (m110) cc_final: 0.7618 (m110)
REVERT: B  490 LEU cc_start: 0.8870 (tp) cc_final: 0.8346 (tp)
REVERT: B  519 ASN cc_start: 0.8504 (t0) cc_final: 0.7890 (t0)
REVERT: B  574 MET cc_start: 0.7767 (mmm) cc_final: 0.7557 (tpt)
REVERT: B  678 MET cc_start: 0.2551 (mmt) cc_final: 0.1079 (tpp)
REVERT: C    9 LYS cc_start: 0.8077 (tttm) cc_final: 0.7551 (mttm)
REVERT: C   17 ASP cc_start: 0.7817 (t0) cc_final: 0.7377 (t0)
REVERT: C   69 GLU cc_start: 0.7931 (pt0) cc_final: 0.7634 (pt0)
REVERT: C  246 PHE cc_start: 0.9170 (m-10) cc_final: 0.8924 (m-10)
REVERT: C  249 ILE cc_start: 0.8513 (tt) cc_final: 0.8085 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 398
  average time/residue: 0.1209
  time to fit residues: 69.8599
Evaluate side-chains
  314 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 314
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 154 optimal weight:    0.0060
   chunk 68 optimal weight:    0.0470
   chunk 148 optimal weight:    0.9990
   chunk 72 optimal weight:    0.6980
   chunk 111 optimal weight:    0.8980
   chunk 133 optimal weight:    5.9990
   chunk 167 optimal weight:   10.0000
   overall best weight:    0.5296

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 638 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 660 HIS
** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 216 HIS
C 240 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.129292 restraints weight = 25567.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.132595 restraints weight = 14526.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.134822 restraints weight = 9722.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136292 restraints weight = 7305.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.136989 restraints weight = 5997.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14441  Z= 0.129
  Angle     :  0.625   8.580  19533  Z= 0.324
  Chirality :  0.043   0.234   2142
  Planarity :  0.004   0.060   2391
  Dihedral  : 12.616 168.529   2227
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.78 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.50 %
    Favored  : 97.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.19), residues: 1653
  helix: -0.87 (0.18), residues: 741
  sheet: -1.04 (0.47), residues: 131
  loop : -2.97 (0.19), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 220 
 TYR   0.012   0.001   TYR A 637 
 PHE   0.016   0.001   PHE A 341 
 TRP   0.016   0.001   TRP A 386 
 HIS   0.008   0.001   HIS C 216 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 (14441)
  covalent geometry    : angle       0.62471 /  0.32 (19533)
  hydrogen bonds       : bond        0.04520 /  2.88 (  583)
  hydrogen bonds       : angle       5.67409 /  4.03 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 379
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7117 (ptp90)
REVERT: A   34 THR cc_start: 0.8509 (p) cc_final: 0.8093 (t)
REVERT: A  357 TRP cc_start: 0.5889 (t60) cc_final: 0.5585 (t60)
REVERT: A  365 PHE cc_start: 0.6860 (t80) cc_final: 0.6415 (t80)
REVERT: A  439 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7971 (tp30)
REVERT: A  442 LYS cc_start: 0.9087 (tttt) cc_final: 0.8607 (ttmm)
REVERT: A  497 MET cc_start: 0.8461 (mpp) cc_final: 0.7857 (mmt)
REVERT: A  511 ASN cc_start: 0.8609 (t0) cc_final: 0.8229 (t0)
REVERT: A  514 LYS cc_start: 0.8964 (tttt) cc_final: 0.8549 (ttpp)
REVERT: A  516 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: A  561 ASP cc_start: 0.8137 (t70) cc_final: 0.7806 (t70)
REVERT: A  619 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7419 (tmtt)
REVERT: B   96 MET cc_start: 0.8448 (mtt) cc_final: 0.8236 (mtt)
REVERT: B  116 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7384 (mp0)
REVERT: B  130 GLN cc_start: 0.8277 (tp40) cc_final: 0.7419 (tp40)
REVERT: B  140 MET cc_start: 0.7108 (mmm) cc_final: 0.6452 (mmm)
REVERT: B  254 SER cc_start: 0.9040 (p) cc_final: 0.8510 (t)
REVERT: B  289 SER cc_start: 0.8885 (m) cc_final: 0.8577 (p)
REVERT: B  335 MET cc_start: 0.7747 (tpp) cc_final: 0.7469 (tpp)
REVERT: B  336 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8198 (ttmm)
REVERT: B  341 VAL cc_start: 0.7920 (p) cc_final: 0.7563 (p)
REVERT: B  378 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7644 (mmm-85)
REVERT: B  382 MET cc_start: 0.8056 (mtp) cc_final: 0.7819 (mmm)
REVERT: B  413 PHE cc_start: 0.7399 (m-10) cc_final: 0.7197 (m-10)
REVERT: B  423 MET cc_start: 0.8678 (mtm) cc_final: 0.8438 (mtm)
REVERT: B  442 LEU cc_start: 0.8672 (tp) cc_final: 0.8414 (tp)
REVERT: B  479 SER cc_start: 0.8633 (t) cc_final: 0.8406 (t)
REVERT: B  490 LEU cc_start: 0.8851 (tp) cc_final: 0.8309 (tp)
REVERT: B  574 MET cc_start: 0.7901 (mmm) cc_final: 0.7668 (tpt)
REVERT: B  678 MET cc_start: 0.2745 (mmt) cc_final: 0.1236 (ttt)
REVERT: B  715 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8506 (mp0)
REVERT: C    6 THR cc_start: 0.7705 (p) cc_final: 0.6851 (p)
REVERT: C    9 LYS cc_start: 0.7950 (tttm) cc_final: 0.7530 (mttm)
REVERT: C   70 GLU cc_start: 0.8008 (pp20) cc_final: 0.7662 (pp20)
REVERT: C  140 MET cc_start: 0.8592 (mtp) cc_final: 0.8341 (mtm)
REVERT: C  247 TRP cc_start: 0.9059 (p-90) cc_final: 0.8725 (p-90)
  outliers start: 1
  outliers final: 0
  residues processed: 380
  average time/residue: 0.1183
  time to fit residues: 65.9973
Evaluate side-chains
  308 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 136 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 149 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 130 optimal weight:    4.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 GLN
A 170 ASN
A 277 HIS
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 ASN
B 333 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.156999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.124227 restraints weight = 25769.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.127358 restraints weight = 14909.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.129396 restraints weight = 10112.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130585 restraints weight = 7763.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.131565 restraints weight = 6547.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14441  Z= 0.185
  Angle     :  0.667  12.824  19533  Z= 0.344
  Chirality :  0.044   0.209   2142
  Planarity :  0.004   0.055   2391
  Dihedral  : 12.577 168.119   2227
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.38 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.10 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.20), residues: 1653
  helix: -0.29 (0.19), residues: 738
  sheet: -0.93 (0.47), residues: 131
  loop : -2.78 (0.20), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 567 
 TYR   0.020   0.002   TYR B 427 
 PHE   0.028   0.001   PHE A 161 
 TRP   0.016   0.001   TRP A 386 
 HIS   0.009   0.002   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.18 (14441)
  covalent geometry    : angle       0.66660 /  0.34 (19533)
  hydrogen bonds       : bond        0.04633 /  3.01 (  583)
  hydrogen bonds       : angle       5.34956 /  3.81 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 366
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7080 (ptp90)
REVERT: A   34 THR cc_start: 0.8637 (p) cc_final: 0.8116 (t)
REVERT: A  365 PHE cc_start: 0.6840 (t80) cc_final: 0.6440 (t80)
REVERT: A  416 MET cc_start: 0.7897 (ppp) cc_final: 0.7166 (ppp)
REVERT: A  439 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8123 (tp30)
REVERT: A  497 MET cc_start: 0.8502 (mpp) cc_final: 0.7883 (mmt)
REVERT: A  511 ASN cc_start: 0.8771 (t0) cc_final: 0.8422 (t0)
REVERT: A  514 LYS cc_start: 0.9038 (tttt) cc_final: 0.8722 (ttpt)
REVERT: A  516 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: A  561 ASP cc_start: 0.8258 (t70) cc_final: 0.7907 (t70)
REVERT: A  603 TRP cc_start: 0.7296 (m-90) cc_final: 0.6963 (m-90)
REVERT: A  619 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7476 (tmtt)
REVERT: A  654 MET cc_start: 0.8838 (tpp) cc_final: 0.8526 (tpp)
REVERT: B   96 MET cc_start: 0.8703 (mtt) cc_final: 0.8403 (mtt)
REVERT: B  116 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7104 (mp0)
REVERT: B  130 GLN cc_start: 0.8277 (tp40) cc_final: 0.7582 (tp40)
REVERT: B  140 MET cc_start: 0.7384 (mmm) cc_final: 0.6888 (mmm)
REVERT: B  289 SER cc_start: 0.8995 (m) cc_final: 0.8708 (p)
REVERT: B  336 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8166 (ttmm)
REVERT: B  341 VAL cc_start: 0.8123 (p) cc_final: 0.7758 (p)
REVERT: B  378 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7819 (mmm-85)
REVERT: B  382 MET cc_start: 0.7986 (mtp) cc_final: 0.7732 (mmm)
REVERT: B  383 ASN cc_start: 0.8136 (m110) cc_final: 0.7649 (m110)
REVERT: B  423 MET cc_start: 0.8734 (mtm) cc_final: 0.8512 (mtm)
REVERT: B  442 LEU cc_start: 0.8726 (tp) cc_final: 0.8505 (mp)
REVERT: B  490 LEU cc_start: 0.8861 (tp) cc_final: 0.8294 (tp)
REVERT: B  574 MET cc_start: 0.8014 (mmm) cc_final: 0.7800 (tpt)
REVERT: B  678 MET cc_start: 0.2875 (mmt) cc_final: 0.1412 (ttt)
REVERT: C    6 THR cc_start: 0.7695 (p) cc_final: 0.6650 (p)
REVERT: C    9 LYS cc_start: 0.8029 (tttm) cc_final: 0.7578 (mttm)
REVERT: C   70 GLU cc_start: 0.8084 (pp20) cc_final: 0.7850 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 367
  average time/residue: 0.1167
  time to fit residues: 63.4426
Evaluate side-chains
  293 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 293
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 95 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 115 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 128 optimal weight:    4.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.154350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.122797 restraints weight = 25522.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.125875 restraints weight = 14635.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.127911 restraints weight = 9875.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.129282 restraints weight = 7523.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130141 restraints weight = 6238.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14441  Z= 0.158
  Angle     :  0.638   7.741  19533  Z= 0.333
  Chirality :  0.044   0.260   2142
  Planarity :  0.004   0.056   2391
  Dihedral  : 12.527 167.813   2227
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.50 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.62 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.20), residues: 1653
  helix: -0.07 (0.19), residues: 740
  sheet: -0.91 (0.47), residues: 129
  loop : -2.69 (0.20), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 129 
 TYR   0.010   0.001   TYR B 427 
 PHE   0.053   0.002   PHE C 190 
 TRP   0.017   0.001   TRP C 247 
 HIS   0.003   0.001   HIS A 263 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 (14441)
  covalent geometry    : angle       0.63768 /  0.33 (19533)
  hydrogen bonds       : bond        0.04462 /  2.87 (  583)
  hydrogen bonds       : angle       5.13802 /  3.66 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 347
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7210 (ptp90)
REVERT: A   34 THR cc_start: 0.8634 (p) cc_final: 0.8072 (t)
REVERT: A   47 LEU cc_start: 0.8563 (tp) cc_final: 0.8360 (tp)
REVERT: A  365 PHE cc_start: 0.6942 (t80) cc_final: 0.6548 (t80)
REVERT: A  416 MET cc_start: 0.8294 (ppp) cc_final: 0.7351 (ppp)
REVERT: A  439 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8136 (tp30)
REVERT: A  497 MET cc_start: 0.8476 (mpp) cc_final: 0.7860 (mmt)
REVERT: A  511 ASN cc_start: 0.8790 (t0) cc_final: 0.8436 (t0)
REVERT: A  516 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7737 (tm-30)
REVERT: A  561 ASP cc_start: 0.8365 (t70) cc_final: 0.8023 (t70)
REVERT: A  619 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7387 (tmtt)
REVERT: A  654 MET cc_start: 0.8863 (tpp) cc_final: 0.8453 (tpp)
REVERT: B  116 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7111 (mp0)
REVERT: B  123 SER cc_start: 0.8246 (p) cc_final: 0.7998 (p)
REVERT: B  254 SER cc_start: 0.9109 (p) cc_final: 0.8605 (t)
REVERT: B  289 SER cc_start: 0.9003 (m) cc_final: 0.8698 (p)
REVERT: B  336 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8114 (ttmm)
REVERT: B  341 VAL cc_start: 0.7954 (p) cc_final: 0.7557 (p)
REVERT: B  378 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7843 (mmm-85)
REVERT: B  382 MET cc_start: 0.8139 (mtp) cc_final: 0.7850 (mmm)
REVERT: B  383 ASN cc_start: 0.8117 (m110) cc_final: 0.7853 (m110)
REVERT: B  413 PHE cc_start: 0.7699 (m-10) cc_final: 0.7431 (m-80)
REVERT: B  415 MET cc_start: 0.7508 (mtt) cc_final: 0.7219 (mtt)
REVERT: B  423 MET cc_start: 0.8716 (mtm) cc_final: 0.8449 (mtm)
REVERT: B  479 SER cc_start: 0.8795 (t) cc_final: 0.8515 (p)
REVERT: B  490 LEU cc_start: 0.8769 (tp) cc_final: 0.8330 (tp)
REVERT: B  522 THR cc_start: 0.8849 (p) cc_final: 0.8471 (t)
REVERT: B  678 MET cc_start: 0.2864 (mmt) cc_final: 0.1216 (ttt)
REVERT: C    6 THR cc_start: 0.7612 (p) cc_final: 0.7109 (p)
REVERT: C   17 ASP cc_start: 0.7316 (t0) cc_final: 0.6931 (t0)
REVERT: C   70 GLU cc_start: 0.8090 (pp20) cc_final: 0.7852 (pp20)
REVERT: C  140 MET cc_start: 0.8595 (mtp) cc_final: 0.8245 (mtm)
REVERT: C  247 TRP cc_start: 0.9165 (p-90) cc_final: 0.8781 (p-90)
  outliers start: 1
  outliers final: 0
  residues processed: 348
  average time/residue: 0.1226
  time to fit residues: 62.7960
Evaluate side-chains
  284 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 284
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 109 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 121 optimal weight:    0.3980
   chunk 119 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0270
   overall best weight:    0.6038

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
A 222 GLN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
B 333 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.158617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.127367 restraints weight = 25532.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.130067 restraints weight = 15417.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132323 restraints weight = 9704.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.132933 restraints weight = 7952.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.132870 restraints weight = 6565.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14441  Z= 0.122
  Angle     :  0.621   7.877  19533  Z= 0.321
  Chirality :  0.043   0.227   2142
  Planarity :  0.004   0.057   2391
  Dihedral  : 12.473 167.674   2227
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.14 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  1.56 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.20), residues: 1653
  helix:  0.15 (0.19), residues: 737
  sheet: -0.91 (0.49), residues: 119
  loop : -2.57 (0.20), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 220 
 TYR   0.010   0.001   TYR C  11 
 PHE   0.035   0.001   PHE C 190 
 TRP   0.019   0.001   TRP A 562 
 HIS   0.003   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.12 (14441)
  covalent geometry    : angle       0.62149 /  0.32 (19533)
  hydrogen bonds       : bond        0.04167 /  2.66 (  583)
  hydrogen bonds       : angle       4.95399 /  3.54 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 355
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7367 (ttp80) cc_final: 0.7028 (ptp90)
REVERT: A   34 THR cc_start: 0.8578 (p) cc_final: 0.8009 (t)
REVERT: A   47 LEU cc_start: 0.8520 (tp) cc_final: 0.8265 (tp)
REVERT: A  350 LYS cc_start: 0.8456 (ttpt) cc_final: 0.8147 (ttpp)
REVERT: A  365 PHE cc_start: 0.7064 (t80) cc_final: 0.6670 (t80)
REVERT: A  416 MET cc_start: 0.8381 (ppp) cc_final: 0.7378 (ppp)
REVERT: A  497 MET cc_start: 0.8424 (mpp) cc_final: 0.7810 (mmt)
REVERT: A  511 ASN cc_start: 0.8781 (t0) cc_final: 0.8414 (t0)
REVERT: A  516 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: A  561 ASP cc_start: 0.8366 (t70) cc_final: 0.8026 (t70)
REVERT: A  619 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8086 (mmtp)
REVERT: A  654 MET cc_start: 0.8926 (tpp) cc_final: 0.8326 (tpp)
REVERT: B  116 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7147 (mp0)
REVERT: B  123 SER cc_start: 0.8247 (p) cc_final: 0.7955 (p)
REVERT: B  130 GLN cc_start: 0.8264 (tp40) cc_final: 0.7473 (tp40)
REVERT: B  140 MET cc_start: 0.7310 (mmm) cc_final: 0.6572 (mmm)
REVERT: B  254 SER cc_start: 0.9104 (p) cc_final: 0.8583 (t)
REVERT: B  289 SER cc_start: 0.9019 (m) cc_final: 0.8679 (p)
REVERT: B  336 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8202 (ttmm)
REVERT: B  341 VAL cc_start: 0.8025 (p) cc_final: 0.7684 (p)
REVERT: B  378 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7825 (mmm-85)
REVERT: B  382 MET cc_start: 0.8096 (mtp) cc_final: 0.7797 (mmm)
REVERT: B  383 ASN cc_start: 0.8130 (m110) cc_final: 0.7767 (m110)
REVERT: B  413 PHE cc_start: 0.7607 (m-10) cc_final: 0.7277 (m-80)
REVERT: B  415 MET cc_start: 0.7408 (mtt) cc_final: 0.7102 (mtt)
REVERT: B  423 MET cc_start: 0.8623 (mtm) cc_final: 0.8385 (mtm)
REVERT: B  479 SER cc_start: 0.8787 (t) cc_final: 0.8536 (p)
REVERT: B  490 LEU cc_start: 0.8738 (tp) cc_final: 0.8272 (tp)
REVERT: B  522 THR cc_start: 0.8876 (p) cc_final: 0.8490 (t)
REVERT: B  678 MET cc_start: 0.2629 (mmt) cc_final: 0.1560 (ttt)
REVERT: B  717 LYS cc_start: 0.8519 (tppt) cc_final: 0.8290 (tppt)
REVERT: C    6 THR cc_start: 0.7588 (p) cc_final: 0.6979 (p)
REVERT: C    9 LYS cc_start: 0.8086 (tttm) cc_final: 0.7582 (mttm)
REVERT: C  247 TRP cc_start: 0.9102 (p-90) cc_final: 0.8760 (p-90)
  outliers start: 1
  outliers final: 1
  residues processed: 356
  average time/residue: 0.1213
  time to fit residues: 63.7183
Evaluate side-chains
  287 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 286
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 143 optimal weight:    0.1980
   chunk 25 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 146 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 160 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0030
   chunk 141 optimal weight:    4.9990
   chunk 103 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7594

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 299 GLN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 742 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.158439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.125929 restraints weight = 25671.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129127 restraints weight = 14897.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131215 restraints weight = 10153.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.132600 restraints weight = 7777.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.133379 restraints weight = 6478.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14441  Z= 0.120
  Angle     :  0.613   7.775  19533  Z= 0.316
  Chirality :  0.043   0.216   2142
  Planarity :  0.004   0.056   2391
  Dihedral  : 12.428 167.490   2227
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.90 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.20), residues: 1653
  helix:  0.30 (0.19), residues: 735
  sheet: -0.72 (0.49), residues: 118
  loop : -2.50 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 129 
 TYR   0.010   0.001   TYR B 560 
 PHE   0.027   0.001   PHE C 190 
 TRP   0.011   0.001   TRP A 386 
 HIS   0.009   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (14441)
  covalent geometry    : angle       0.61343 /  0.32 (19533)
  hydrogen bonds       : bond        0.04099 /  2.61 (  583)
  hydrogen bonds       : angle       4.87166 /  3.47 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 345
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7405 (ttp80) cc_final: 0.6832 (ptp90)
REVERT: A   34 THR cc_start: 0.8637 (p) cc_final: 0.8095 (t)
REVERT: A   47 LEU cc_start: 0.8674 (tp) cc_final: 0.8341 (tt)
REVERT: A  350 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8158 (ttpp)
REVERT: A  365 PHE cc_start: 0.6967 (t80) cc_final: 0.6585 (t80)
REVERT: A  428 GLU cc_start: 0.8180 (tp30) cc_final: 0.7824 (tp30)
REVERT: A  497 MET cc_start: 0.8406 (mpp) cc_final: 0.7759 (mmt)
REVERT: A  511 ASN cc_start: 0.8789 (t0) cc_final: 0.8377 (t0)
REVERT: A  514 LYS cc_start: 0.9057 (tttt) cc_final: 0.8690 (ttpt)
REVERT: A  516 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: A  561 ASP cc_start: 0.8342 (t70) cc_final: 0.8015 (t70)
REVERT: A  603 TRP cc_start: 0.7189 (m-90) cc_final: 0.6832 (m-90)
REVERT: A  619 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8028 (mmtp)
REVERT: A  627 LEU cc_start: 0.9272 (mt) cc_final: 0.8986 (mt)
REVERT: A  648 GLU cc_start: 0.8367 (mp0) cc_final: 0.8022 (mt-10)
REVERT: A  654 MET cc_start: 0.8874 (tpp) cc_final: 0.8432 (tpp)
REVERT: B  116 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7115 (mp0)
REVERT: B  130 GLN cc_start: 0.8273 (tp40) cc_final: 0.7649 (tp40)
REVERT: B  254 SER cc_start: 0.9090 (p) cc_final: 0.8547 (t)
REVERT: B  289 SER cc_start: 0.8971 (m) cc_final: 0.8658 (p)
REVERT: B  336 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8061 (ttmm)
REVERT: B  341 VAL cc_start: 0.7862 (p) cc_final: 0.7507 (p)
REVERT: B  382 MET cc_start: 0.8091 (mtp) cc_final: 0.7854 (mmm)
REVERT: B  413 PHE cc_start: 0.7565 (m-10) cc_final: 0.7266 (m-80)
REVERT: B  423 MET cc_start: 0.8719 (mtm) cc_final: 0.8493 (mtm)
REVERT: B  479 SER cc_start: 0.8795 (t) cc_final: 0.8549 (t)
REVERT: B  490 LEU cc_start: 0.8821 (tp) cc_final: 0.8291 (tp)
REVERT: B  522 THR cc_start: 0.8830 (p) cc_final: 0.8463 (t)
REVERT: B  547 MET cc_start: 0.8413 (ttm) cc_final: 0.8127 (ttt)
REVERT: B  574 MET cc_start: 0.8096 (mmm) cc_final: 0.7621 (tpt)
REVERT: B  678 MET cc_start: 0.2770 (mmt) cc_final: 0.1517 (ttt)
REVERT: C    6 THR cc_start: 0.7574 (p) cc_final: 0.6929 (p)
REVERT: C    9 LYS cc_start: 0.8154 (tttm) cc_final: 0.7605 (mttm)
REVERT: C   17 ASP cc_start: 0.7309 (t0) cc_final: 0.6890 (t0)
REVERT: C  247 TRP cc_start: 0.9072 (p-90) cc_final: 0.8823 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 345
  average time/residue: 0.1143
  time to fit residues: 58.3380
Evaluate side-chains
  283 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 159 optimal weight:    2.9990
   chunk 152 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 156 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 ASN
B 333 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 742 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.155618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.123256 restraints weight = 25859.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.126326 restraints weight = 15072.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.128378 restraints weight = 10340.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129609 restraints weight = 7938.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.130596 restraints weight = 6676.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14441  Z= 0.170
  Angle     :  0.656   8.401  19533  Z= 0.339
  Chirality :  0.044   0.259   2142
  Planarity :  0.004   0.057   2391
  Dihedral  : 12.431 167.393   2227
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.38 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.61 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.20), residues: 1653
  helix:  0.32 (0.19), residues: 740
  sheet: -0.73 (0.49), residues: 119
  loop : -2.55 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 665 
 TYR   0.023   0.001   TYR B 350 
 PHE   0.024   0.002   PHE C 190 
 TRP   0.014   0.001   TRP A 386 
 HIS   0.005   0.001   HIS A 277 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00392 /  0.17 (14441)
  covalent geometry    : angle       0.65638 /  0.34 (19533)
  hydrogen bonds       : bond        0.04296 /  2.75 (  583)
  hydrogen bonds       : angle       4.86786 /  3.45 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 340
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6861 (ptp90)
REVERT: A   34 THR cc_start: 0.8675 (p) cc_final: 0.8158 (t)
REVERT: A   47 LEU cc_start: 0.8561 (tp) cc_final: 0.8279 (tt)
REVERT: A  350 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8230 (ttpp)
REVERT: A  365 PHE cc_start: 0.7022 (t80) cc_final: 0.6639 (t80)
REVERT: A  497 MET cc_start: 0.8395 (mpp) cc_final: 0.7747 (mmt)
REVERT: A  511 ASN cc_start: 0.8842 (t0) cc_final: 0.8480 (t0)
REVERT: A  516 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7907 (tm-30)
REVERT: A  565 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8479 (mtmm)
REVERT: A  584 GLU cc_start: 0.7813 (tp30) cc_final: 0.7585 (tp30)
REVERT: A  603 TRP cc_start: 0.7237 (m-90) cc_final: 0.6905 (m-90)
REVERT: A  654 MET cc_start: 0.8952 (tpp) cc_final: 0.8481 (tpp)
REVERT: B  116 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7089 (mp0)
REVERT: B  123 SER cc_start: 0.8351 (p) cc_final: 0.8088 (p)
REVERT: B  130 GLN cc_start: 0.8236 (tp40) cc_final: 0.7607 (tp40)
REVERT: B  254 SER cc_start: 0.9097 (p) cc_final: 0.8600 (t)
REVERT: B  289 SER cc_start: 0.8958 (m) cc_final: 0.8628 (p)
REVERT: B  301 MET cc_start: 0.8378 (ttm) cc_final: 0.8142 (ttm)
REVERT: B  336 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8188 (ttmm)
REVERT: B  341 VAL cc_start: 0.7885 (p) cc_final: 0.7589 (p)
REVERT: B  415 MET cc_start: 0.7488 (mtt) cc_final: 0.7206 (mtt)
REVERT: B  423 MET cc_start: 0.8920 (mtm) cc_final: 0.8660 (mtm)
REVERT: B  490 LEU cc_start: 0.8837 (tp) cc_final: 0.8371 (tp)
REVERT: B  522 THR cc_start: 0.8891 (p) cc_final: 0.8544 (t)
REVERT: B  547 MET cc_start: 0.8507 (ttm) cc_final: 0.8151 (ttt)
REVERT: B  574 MET cc_start: 0.8080 (mmm) cc_final: 0.7618 (tpt)
REVERT: B  678 MET cc_start: 0.2499 (mmt) cc_final: 0.0973 (ttt)
REVERT: C  247 TRP cc_start: 0.9114 (p-90) cc_final: 0.8847 (p-90)
  outliers start: 1
  outliers final: 0
  residues processed: 341
  average time/residue: 0.1093
  time to fit residues: 55.9691
Evaluate side-chains
  279 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0470
   chunk 54 optimal weight:    0.8980
   chunk 157 optimal weight:    0.0030
   chunk 36 optimal weight:    0.0070
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 128 optimal weight:    0.0270
   chunk 140 optimal weight:    7.9990
   chunk 86 optimal weight:    4.9990
   chunk 148 optimal weight:    2.9990
   overall best weight:    0.1964

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 640 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  46 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.159383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.126697 restraints weight = 25946.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.129879 restraints weight = 15091.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.132021 restraints weight = 10297.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133435 restraints weight = 7877.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.134257 restraints weight = 6582.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14441  Z= 0.117
  Angle     :  0.635   8.262  19533  Z= 0.326
  Chirality :  0.042   0.250   2142
  Planarity :  0.004   0.058   2391
  Dihedral  : 12.399 167.335   2227
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.47 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.34 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.43 (0.20), residues: 1653
  helix:  0.44 (0.19), residues: 740
  sheet: -0.55 (0.48), residues: 119
  loop : -2.47 (0.20), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 129 
 TYR   0.016   0.001   TYR B 350 
 PHE   0.027   0.001   PHE B 524 
 TRP   0.031   0.001   TRP A 357 
 HIS   0.010   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.12 (14441)
  covalent geometry    : angle       0.63496 /  0.33 (19533)
  hydrogen bonds       : bond        0.03951 /  2.50 (  583)
  hydrogen bonds       : angle       4.72363 /  3.35 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 346
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7494 (ttp80) cc_final: 0.6829 (ptp90)
REVERT: A   34 THR cc_start: 0.8706 (p) cc_final: 0.8249 (t)
REVERT: A   47 LEU cc_start: 0.8462 (tp) cc_final: 0.8244 (tt)
REVERT: A  235 ARG cc_start: 0.6549 (tpp-160) cc_final: 0.5751 (tpm170)
REVERT: A  350 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8224 (ttpp)
REVERT: A  358 GLN cc_start: 0.7742 (mp10) cc_final: 0.7467 (mp10)
REVERT: A  365 PHE cc_start: 0.7016 (t80) cc_final: 0.6593 (t80)
REVERT: A  428 GLU cc_start: 0.8076 (tp30) cc_final: 0.7871 (tp30)
REVERT: A  497 MET cc_start: 0.8274 (mpp) cc_final: 0.7643 (mmt)
REVERT: A  511 ASN cc_start: 0.8780 (t0) cc_final: 0.8389 (t0)
REVERT: A  514 LYS cc_start: 0.9039 (tttt) cc_final: 0.8666 (ttpt)
REVERT: A  516 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7827 (tm-30)
REVERT: A  561 ASP cc_start: 0.8405 (t70) cc_final: 0.8169 (t70)
REVERT: A  584 GLU cc_start: 0.7767 (tp30) cc_final: 0.7428 (tp30)
REVERT: A  619 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8110 (mmtp)
REVERT: A  627 LEU cc_start: 0.9220 (mt) cc_final: 0.8944 (mt)
REVERT: B   96 MET cc_start: 0.7816 (mtt) cc_final: 0.7496 (mtt)
REVERT: B  116 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6869 (mp0)
REVERT: B  130 GLN cc_start: 0.8316 (tp40) cc_final: 0.7605 (tp40)
REVERT: B  140 MET cc_start: 0.7281 (mmm) cc_final: 0.6673 (mmm)
REVERT: B  254 SER cc_start: 0.9153 (p) cc_final: 0.8688 (t)
REVERT: B  289 SER cc_start: 0.8920 (m) cc_final: 0.8581 (p)
REVERT: B  336 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8051 (ttmm)
REVERT: B  341 VAL cc_start: 0.7651 (p) cc_final: 0.7301 (p)
REVERT: B  415 MET cc_start: 0.7340 (mtt) cc_final: 0.7076 (mtt)
REVERT: B  423 MET cc_start: 0.8683 (mtm) cc_final: 0.7949 (mtm)
REVERT: B  490 LEU cc_start: 0.8837 (tp) cc_final: 0.8380 (tp)
REVERT: B  522 THR cc_start: 0.8898 (p) cc_final: 0.8479 (t)
REVERT: B  547 MET cc_start: 0.8412 (ttm) cc_final: 0.8038 (ttt)
REVERT: B  574 MET cc_start: 0.8024 (mmm) cc_final: 0.7613 (tpt)
REVERT: B  665 ARG cc_start: 0.7769 (ptm-80) cc_final: 0.7557 (ptt90)
REVERT: B  741 ARG cc_start: 0.7982 (ttm110) cc_final: 0.7695 (ptp-170)
REVERT: C   17 ASP cc_start: 0.7051 (t0) cc_final: 0.6693 (t0)
REVERT: C   32 TYR cc_start: 0.5655 (t80) cc_final: 0.5266 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 347
  average time/residue: 0.1181
  time to fit residues: 60.7955
Evaluate side-chains
  292 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 292
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 114 optimal weight:    0.2980
   chunk 117 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 151 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 137 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 145 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 ASN
B 333 ASN
** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.157984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.125760 restraints weight = 25758.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.128914 restraints weight = 14856.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130975 restraints weight = 10126.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132359 restraints weight = 7771.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.133282 restraints weight = 6488.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.4696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14441  Z= 0.135
  Angle     :  0.670   9.016  19533  Z= 0.344
  Chirality :  0.043   0.264   2142
  Planarity :  0.004   0.058   2391
  Dihedral  : 12.381 167.255   2227
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.84 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.47 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.20), residues: 1653
  helix:  0.47 (0.19), residues: 735
  sheet: -0.35 (0.49), residues: 118
  loop : -2.40 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 129 
 TYR   0.018   0.001   TYR B 350 
 PHE   0.032   0.002   PHE C  35 
 TRP   0.025   0.001   TRP A 357 
 HIS   0.004   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 (14441)
  covalent geometry    : angle       0.67023 /  0.34 (19533)
  hydrogen bonds       : bond        0.03990 /  2.52 (  583)
  hydrogen bonds       : angle       4.71290 /  3.34 ( 1618)

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

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

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3306 Ramachandran restraints generated.
    1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 337
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6881 (ptp90)
REVERT: A   34 THR cc_start: 0.8684 (p) cc_final: 0.8148 (t)
REVERT: A   47 LEU cc_start: 0.8480 (tp) cc_final: 0.8253 (tt)
REVERT: A  235 ARG cc_start: 0.6528 (tpp-160) cc_final: 0.5403 (tpm170)
REVERT: A  350 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8203 (ttpp)
REVERT: A  365 PHE cc_start: 0.6995 (t80) cc_final: 0.6549 (t80)
REVERT: A  416 MET cc_start: 0.8441 (ppp) cc_final: 0.7398 (ppp)
REVERT: A  428 GLU cc_start: 0.8152 (tp30) cc_final: 0.7871 (tp30)
REVERT: A  497 MET cc_start: 0.8300 (mpp) cc_final: 0.7685 (mmt)
REVERT: A  511 ASN cc_start: 0.8825 (t0) cc_final: 0.8418 (t0)
REVERT: A  514 LYS cc_start: 0.9077 (tttt) cc_final: 0.8703 (ttpt)
REVERT: A  516 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: A  561 ASP cc_start: 0.8457 (t70) cc_final: 0.8185 (t70)
REVERT: A  650 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7890 (mtmm)
REVERT: B  116 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6499 (mp0)
REVERT: B  130 GLN cc_start: 0.8329 (tp40) cc_final: 0.7571 (tp40)
REVERT: B  140 MET cc_start: 0.7340 (mmm) cc_final: 0.6680 (mmm)
REVERT: B  220 ILE cc_start: 0.9354 (mm) cc_final: 0.9034 (tp)
REVERT: B  254 SER cc_start: 0.9161 (p) cc_final: 0.8648 (t)
REVERT: B  289 SER cc_start: 0.8911 (m) cc_final: 0.8582 (p)
REVERT: B  336 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8146 (ttmm)
REVERT: B  341 VAL cc_start: 0.7959 (p) cc_final: 0.7684 (p)
REVERT: B  381 LEU cc_start: 0.8405 (mp) cc_final: 0.7343 (mp)
REVERT: B  382 MET cc_start: 0.7779 (mmm) cc_final: 0.7241 (mmm)
REVERT: B  401 CYS cc_start: 0.7432 (t) cc_final: 0.7125 (t)
REVERT: B  415 MET cc_start: 0.7389 (mtt) cc_final: 0.7077 (mtt)
REVERT: B  423 MET cc_start: 0.8835 (mtm) cc_final: 0.8564 (mtm)
REVERT: B  490 LEU cc_start: 0.8918 (tp) cc_final: 0.8428 (tp)
REVERT: B  522 THR cc_start: 0.9208 (p) cc_final: 0.8749 (t)
REVERT: B  574 MET cc_start: 0.8017 (mmm) cc_final: 0.7582 (tpt)
REVERT: B  678 MET cc_start: 0.2753 (mmt) cc_final: 0.1076 (ttt)
REVERT: B  741 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7493 (ptp-170)
REVERT: C  140 MET cc_start: 0.7599 (ttm) cc_final: 0.7245 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 338
  average time/residue: 0.1191
  time to fit residues: 59.5238
Evaluate side-chains
  290 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 289
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 133 optimal weight:    7.9990
   chunk 79 optimal weight:    0.5980
   chunk 98 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0170
   chunk 127 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 141 optimal weight:    8.9990
   chunk 132 optimal weight:    2.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 HIS
A 170 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 296 ASN
** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 383 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.159112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126315 restraints weight = 25932.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.129471 restraints weight = 15144.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131559 restraints weight = 10381.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132851 restraints weight = 7983.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.133812 restraints weight = 6721.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.4825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14441  Z= 0.123
  Angle     :  0.658   9.542  19533  Z= 0.338
  Chirality :  0.043   0.254   2142
  Planarity :  0.004   0.058   2391
  Dihedral  : 12.376 167.198   2227
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  6.96 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.27 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.20), residues: 1653
  helix:  0.48 (0.19), residues: 733
  sheet: -0.34 (0.49), residues: 121
  loop : -2.33 (0.21), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 129 
 TYR   0.021   0.001   TYR A  52 
 PHE   0.031   0.002   PHE B 413 
 TRP   0.023   0.001   TRP A 357 
 HIS   0.010   0.001   HIS A  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (14441)
  covalent geometry    : angle       0.65808 /  0.34 (19533)
  hydrogen bonds       : bond        0.03950 /  2.47 (  583)
  hydrogen bonds       : angle       4.70675 /  3.34 ( 1618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.03 seconds
wall clock time: 42 minutes 47.88 seconds (2567.88 seconds total)