Starting phenix.real_space_refine
on Wed Mar  4 14:38:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t0r_10357/03_2026/6t0r_10357.cif"
  }
  resolution = 2.82
  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=   0.000 sd=   0.004
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      20      5.49       5
     S      92      5.16       5
     C    8826      2.51       5
     N    2460      2.21       5
     O    2722      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14120
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5724
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 701, 5716
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 25, 'TRANS': 675}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 701, 5716
          Classifications: {'peptide': 701}
          Link IDs: {'PTRANS': 25, 'TRANS': 675}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 5828
    Chain: "B"
      Number of atoms: 5919
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 5919
          Classifications: {'peptide': 739}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 710}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 2016
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 12, 'TRANS': 237}
    Chain: "V"
      Number of atoms: 430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 430
          Classifications: {'RNA': 20}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 10, 'rna3p': 9}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "B"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "V"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 4.09, per 1000 atoms: 0.29
  Number of scatterers: 14120
  At special positions: 0
  Unit cell: (94.2732, 118.654, 117.841, 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      92     16.00
     P      20     15.00
     O    2722      8.00
     N    2460      7.00
     C    8826      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: 1.59
  Conformation dependent library (CDL) restraints added in 926.8 milliseconds
  

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3194

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 17 sheets defined
      50.3% alpha, 12.5% beta
      2 base pairs and 8 stacking pairs defined.
    Time for finding SS restraints: 1.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 9
      removed outlier: 3.648A  pdb=" N   ARG A   6 " --> pdb=" O   GLU A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 10 through 25
    Processing helix  chain 'A' and resid 32 through 50
    Processing helix  chain 'A' and resid 83 through 98
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.657A  pdb=" N   TYR A 130 " --> pdb=" O   LYS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 160
      No H-bonds generated for 'chain 'A' and resid 158 through 160'
    Processing helix  chain 'A' and resid 164 through 185
    Processing helix  chain 'A' and resid 188 through 193
      removed outlier: 4.046A  pdb=" N   ARG A 192 " --> pdb=" O   TRP A 188 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   GLN A 193 " --> pdb=" O   ASP A 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 188 through 193'
    Processing helix  chain 'A' and resid 208 through 216
    Processing helix  chain 'A' and resid 225 through 235
    Processing helix  chain 'A' and resid 240 through 248
      removed outlier: 3.602A  pdb=" N   ALA A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 330 through 347
      removed outlier: 3.627A  pdb=" N   TYR A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 365
    Processing helix  chain 'A' and resid 399 through 410
      removed outlier: 4.548A  pdb=" N   GLN A 403 " --> pdb=" O   ALA A 399 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A 410 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 446
    Processing helix  chain 'A' and resid 448 through 471
      removed outlier: 3.533A  pdb=" N   GLU A 452 " --> pdb=" O   CYS A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 575
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 4.053A  pdb=" N   VAL A 597 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'A' and resid 627 through 645
    Processing helix  chain 'A' and resid 647 through 669
      removed outlier: 4.505A  pdb=" N   LYS A 659 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 660 " --> pdb=" O   GLU A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 688
      removed outlier: 4.072A  pdb=" N   CYS A 688 " --> pdb=" O   ALA A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 712
    Processing helix  chain 'B' and resid 5 through 11
    Processing helix  chain 'B' and resid 14 through 22
      removed outlier: 3.964A  pdb=" N   ILE B  18 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   SER B  19 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE B  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 49
    Processing helix  chain 'B' and resid 84 through 99
    Processing helix  chain 'B' and resid 101 through 115
      removed outlier: 3.623A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 124
      removed outlier: 3.786A  pdb=" N   LYS B 121 " --> pdb=" O   ARG B 118 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN B 124 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 162 through 173
      removed outlier: 3.524A  pdb=" N   PHE B 166 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 176
      No H-bonds generated for 'chain 'B' and resid 174 through 176'
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 248 through 264
    Processing helix  chain 'B' and resid 275 through 289
      removed outlier: 3.975A  pdb=" N   LYS B 279 " --> pdb=" O   GLY B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 313
      removed outlier: 3.682A  pdb=" N   ASN B 312 " --> pdb=" O   LYS B 308 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLN B 313 " --> pdb=" O   TRP B 309 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 308 through 313'
    Processing helix  chain 'B' and resid 314 through 326
    Processing helix  chain 'B' and resid 330 through 346
      removed outlier: 4.729A  pdb=" N   ALA B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 377 through 381
      removed outlier: 3.559A  pdb=" N   TYR B 380 " --> pdb=" O   ASN B 377 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 381 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 377 through 381'
    Processing helix  chain 'B' and resid 382 through 393
    Processing helix  chain 'B' and resid 412 through 427
      removed outlier: 3.577A  pdb=" N   SER B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLY B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 433
    Processing helix  chain 'B' and resid 455 through 473
      removed outlier: 3.502A  pdb=" N   VAL B 473 " --> pdb=" O   THR B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 536
    Processing helix  chain 'B' and resid 540 through 559
    Processing helix  chain 'B' and resid 572 through 582
      removed outlier: 3.514A  pdb=" N   GLU B 582 " --> pdb=" O   ARG B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.547A  pdb=" N   LEU B 589 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 594
    Processing helix  chain 'B' and resid 607 through 612
    Processing helix  chain 'B' and resid 617 through 625
    Processing helix  chain 'B' and resid 683 through 700
      removed outlier: 3.839A  pdb=" N   ARG B 687 " --> pdb=" O   LEU B 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 732
    Processing helix  chain 'B' and resid 736 through 756
    Processing helix  chain 'C' and resid 1 through 12
    Processing helix  chain 'C' and resid 13 through 23
    Processing helix  chain 'C' and resid 30 through 34
      removed outlier: 3.642A  pdb=" N   TYR C  34 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 52
      removed outlier: 3.735A  pdb=" N   ALA C  52 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 67
      removed outlier: 3.654A  pdb=" N   ILE C  67 " --> pdb=" O   ILE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 103
      removed outlier: 3.891A  pdb=" N   VAL C  96 " --> pdb=" O   SER C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 115
      removed outlier: 4.560A  pdb=" N   ARG C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   TYR C 115 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 127
    Processing helix  chain 'C' and resid 155 through 167
      removed outlier: 4.145A  pdb=" N   GLN C 160 " --> pdb=" O   SER C 156 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   GLU C 161 " --> pdb=" O   ARG C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 172
      removed outlier: 3.893A  pdb=" N   VAL C 172 " --> pdb=" O   PRO C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 193
      removed outlier: 3.711A  pdb=" N   LEU C 183 " --> pdb=" O   SER C 179 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   THR C 184 " --> pdb=" O   ASP C 180 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 212
    Processing helix  chain 'C' and resid 225 through 230
      removed outlier: 3.820A  pdb=" N   GLU C 230 " --> pdb=" O   SER C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 236
      removed outlier: 3.564A  pdb=" N   GLN C 236 " --> pdb=" O   LEU C 232 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.057A  pdb=" N   PHE A 117 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   HIS A 146 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   GLU A 119 " --> pdb=" O   HIS A 146 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   PHE A 148 " --> pdb=" O   GLU A 119 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLY A 121 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ILE A 147 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET A 155 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259
    Processing sheet with id=AA4, first strand: chain 'A' and resid 274 through 275
      removed outlier: 6.466A  pdb=" N   LYS A 274 " --> pdb=" O   LYS A 397 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293
      removed outlier: 7.235A  pdb=" N   TYR A 496 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LEU A 558 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   GLU A 539 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL A 560 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 560 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   VAL A 537 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 293
      removed outlier: 5.403A  pdb=" N   THR A 493 " --> pdb=" O   CYS A 484 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   CYS A 484 " --> pdb=" O   THR A 493 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   LEU A 495 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   THR A 482 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLY A 497 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 476 " --> pdb=" O   LYS A 501 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   TYR A 475 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 374
      removed outlier: 4.349A  pdb=" N   GLN B 367 " --> pdb=" O   MET A 374 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 622 through 626
      removed outlier: 6.338A  pdb=" N   GLY A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   GLU A 618 " --> pdb=" O   GLY A 622 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLU A 624 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP B   2 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 54 through 57
    Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130
      removed outlier: 3.513A  pdb=" N   ARG B 135 " --> pdb=" O   ASP B 130 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 183
    Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 192
      removed outlier: 7.877A  pdb=" N   ASN B 678 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG B 203 " --> pdb=" O   ASN B 678 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243
      removed outlier: 6.969A  pdb=" N   LEU B 224 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491
    Processing sheet with id=AB6, first strand: chain 'C' and resid 57 through 59
    Processing sheet with id=AB7, first strand: chain 'C' and resid 129 through 133
      removed outlier: 4.550A  pdb=" N   GLN C 243 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 141 through 148
      removed outlier: 6.362A  pdb=" N   ARG C 214 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)

    665 hydrogen bonds defined for protein.
    1872 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      5 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      8 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 2.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3789
        1.33 -     1.45: 2601
        1.45 -     1.57: 7829
        1.57 -     1.69: 38
        1.69 -     1.81: 160
  Bond restraints: 14417
  Sorted by residual:
  bond pdb=" C   GLU A 604 "
       pdb=" N   PRO A 605 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.35e+00
  bond pdb=" CB  VAL A 631 "
       pdb=" CG2 VAL A 631 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.30e+00
  bond pdb=" CG1 ILE C  67 "
       pdb=" CD1 ILE C  67 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.31e+00
  bond pdb=" CA  SER A 504 "
       pdb=" CB  SER A 504 "
    ideal  model  delta    sigma   weight residual
    1.539  1.485  0.055 4.88e-02 4.20e+02 1.26e+00
  bond pdb=" CG1 ILE B 389 "
       pdb=" CD1 ILE B 389 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.25e+00
  ... (remaining 14412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 18935
        1.63 -     3.25: 529
        3.25 -     4.88: 48
        4.88 -     6.51: 16
        6.51 -     8.14: 3
  Bond angle restraints: 19531
  Sorted by residual:
  angle pdb=" N   ILE A  79 "
        pdb=" CA  ILE A  79 "
        pdb=" C   ILE A  79 "
      ideal   model   delta    sigma   weight residual
     113.42  108.10    5.32 1.17e+00 7.31e-01 2.07e+01
  angle pdb=" C   HIS A 297 "
        pdb=" N   GLU A 298 "
        pdb=" CA  GLU A 298 "
      ideal   model   delta    sigma   weight residual
     121.54  127.38   -5.84 1.91e+00 2.74e-01 9.36e+00
  angle pdb=" O4'   A V   7 "
        pdb=" C1'   A V   7 "
        pdb=" N9    A V   7 "
      ideal   model   delta    sigma   weight residual
     108.20  112.66   -4.46 1.50e+00 4.44e-01 8.86e+00
  angle pdb=" CA  TYR B 557 "
        pdb=" CB  TYR B 557 "
        pdb=" CG  TYR B 557 "
      ideal   model   delta    sigma   weight residual
     113.90  108.59    5.31 1.80e+00 3.09e-01 8.72e+00
  angle pdb=" CA  SER B 404 "
        pdb=" C   SER B 404 "
        pdb=" N   PRO B 405 "
      ideal   model   delta    sigma   weight residual
     118.44  122.89   -4.45 1.59e+00 3.96e-01 7.82e+00
  ... (remaining 19526 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 7978
       17.81 -    35.62: 602
       35.62 -    53.43: 154
       53.43 -    71.24: 57
       71.24 -    89.05: 14
  Dihedral angle restraints: 8805
    sinusoidal: 3868
      harmonic: 4937
  Sorted by residual:
  dihedral pdb=" CA  THR B 223 "
           pdb=" C   THR B 223 "
           pdb=" N   LEU B 224 "
           pdb=" CA  LEU B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.37   20.63     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ASN A   8 "
           pdb=" C   ASN A   8 "
           pdb=" N   PHE A   9 "
           pdb=" CA  PHE A   9 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.69  -20.31     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  LEU A 219 "
           pdb=" C   LEU A 219 "
           pdb=" N   PRO A 220 "
           pdb=" CA  PRO A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.02   18.98     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 8802 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1485
       0.043 -    0.086: 518
       0.086 -    0.129: 122
       0.129 -    0.172: 13
       0.172 -    0.215: 3
  Chirality restraints: 2141
  Sorted by residual:
  chirality pdb=" CB  ILE B 368 "
            pdb=" CA  ILE B 368 "
            pdb=" CG1 ILE B 368 "
            pdb=" CG2 ILE B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C1'   A V   7 "
            pdb=" O4'   A V   7 "
            pdb=" C2'   A V   7 "
            pdb=" N9    A V   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.18 2.00e-01 2.50e+01 8.54e-01
  chirality pdb=" CB  VAL A 445 "
            pdb=" CA  VAL A 445 "
            pdb=" CG1 VAL A 445 "
            pdb=" CG2 VAL A 445 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.88e-01
  ... (remaining 2138 not shown)

  Planarity restraints: 2439
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 619 "   -0.042 5.00e-02 4.00e+02   6.41e-02 6.57e+00
        pdb=" N   PRO A 620 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 620 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 620 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   7 "   -0.031 2.00e-02 2.50e+03   1.47e-02 5.93e+00
        pdb=" N9    A V   7 "    0.036 2.00e-02 2.50e+03
        pdb=" C8    A V   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    A V   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A V   7 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A V   7 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A V   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    A V   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A V   7 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    A V   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A V   7 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 111 "    0.039 5.00e-02 4.00e+02   5.82e-02 5.41e+00
        pdb=" N   PRO C 112 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO C 112 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 112 "    0.033 5.00e-02 4.00e+02
  ... (remaining 2436 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3824
        2.80 -     3.33: 11808
        3.33 -     3.85: 24720
        3.85 -     4.38: 29485
        4.38 -     4.90: 49848
  Nonbonded interactions: 119685
  Sorted by model distance:
  nonbonded pdb=" O   THR C 224 "
            pdb=" OG1 THR C 224 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLU A 588 "
            pdb=" OG1 THR B 543 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OD2 ASP B 593 "
            pdb=" OH  TYR B 620 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ASN A   3 "
            pdb=" OG1 THR A   7 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ALA B 113 "
            pdb=" OG1 THR B 117 "
     model   vdw
     2.295 3.040
  ... (remaining 119680 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.710
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.800
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
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      :  0.005   0.056  14417  Z= 0.210
  Angle     :  0.662   8.137  19531  Z= 0.389
  Chirality :  0.045   0.215   2141
  Planarity :  0.006   0.064   2439
  Dihedral  : 14.591  89.049   5611
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  :  7.52 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -2.98 (0.16), residues: 1679
  helix: -1.80 (0.14), residues: 764
  sheet: -1.82 (0.34), residues: 189
  loop : -2.07 (0.19), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 578 
 TYR   0.025   0.002   TYR B 557 
 PHE   0.020   0.002   PHE A 515 
 TRP   0.021   0.002   TRP B 438 
 HIS   0.005   0.001   HIS B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (14417)
  covalent geometry    : angle       0.66189 (19531)
  hydrogen bonds       : bond        0.13585 (  666)
  hydrogen bonds       : angle       5.90445 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 294
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.8261 (m-40) cc_final: 0.7870 (m110)
REVERT: A   97 MET cc_start: 0.6944 (tmm) cc_final: 0.6681 (ttt)
REVERT: A  202 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4990 (mp0)
REVERT: A  272 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7086 (mp0)
REVERT: A  419 GLU cc_start: 0.7832 (tp30) cc_final: 0.7630 (tp30)
REVERT: A  616 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8402 (pp)
REVERT: B  669 LYS cc_start: 0.7388 (tttt) cc_final: 0.7121 (tptm)
REVERT: B  672 ARG cc_start: 0.7656 (mtm180) cc_final: 0.7050 (mtt-85)
REVERT: B  709 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7887 (mm)
REVERT: C   15 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7891 (tmt170)
REVERT: C   49 TRP cc_start: 0.8041 (p-90) cc_final: 0.7549 (p90)
REVERT: C   51 MET cc_start: 0.8623 (mmm) cc_final: 0.8256 (mmt)
REVERT: C   82 LYS cc_start: 0.4296 (OUTLIER) cc_final: 0.3441 (mmtt)
  outliers start: 75
  outliers final: 20
  residues processed: 349
  average time/residue: 0.7518
  time to fit residues: 283.0087
Evaluate side-chains
  235 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 210
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 VAL
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  202 GLU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  578 ARG
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  619 ASP
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  739 ASP
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  213 ARG
Chi-restraints excluded: chain C residue  224 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 217 GLN
B 124 GLN
B 314 ASN
B 452 ASN
B 676 ASN
B 690 GLN
C  87 ASN
C 182 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.162973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.132888 restraints weight = 24089.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.06
r_work: 0.3274 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14417  Z= 0.118
  Angle     :  0.508   6.842  19531  Z= 0.273
  Chirality :  0.040   0.199   2141
  Planarity :  0.004   0.047   2439
  Dihedral  : 11.011  76.691   2200
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 15.50 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.03 (0.19), residues: 1679
  helix:  0.35 (0.18), residues: 773
  sheet: -1.24 (0.37), residues: 172
  loop : -1.64 (0.20), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 170 
 TYR   0.024   0.001   TYR B 557 
 PHE   0.015   0.001   PHE A  53 
 TRP   0.020   0.001   TRP C  49 
 HIS   0.002   0.001   HIS B 363 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (14417)
  covalent geometry    : angle       0.50751 (19531)
  hydrogen bonds       : bond        0.03955 (  666)
  hydrogen bonds       : angle       4.23567 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 221
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.8193 (m-40) cc_final: 0.7831 (m110)
REVERT: A   97 MET cc_start: 0.6962 (tmm) cc_final: 0.6535 (ttt)
REVERT: A  153 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6225 (mp0)
REVERT: A  272 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7709 (mp0)
REVERT: A  304 MET cc_start: 0.8389 (mmm) cc_final: 0.8178 (tpt)
REVERT: A  397 LYS cc_start: 0.8791 (tttt) cc_final: 0.8538 (ttpm)
REVERT: A  419 GLU cc_start: 0.8173 (tp30) cc_final: 0.7825 (tp30)
REVERT: A  612 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8436 (m110)
REVERT: A  616 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8386 (pp)
REVERT: B  268 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8157 (mt0)
REVERT: B  669 LYS cc_start: 0.7902 (tttt) cc_final: 0.7643 (tptt)
REVERT: B  672 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7068 (mtt-85)
REVERT: B  680 ARG cc_start: 0.7642 (mtp180) cc_final: 0.6666 (mmt180)
REVERT: B  683 LEU cc_start: 0.7862 (mm) cc_final: 0.7518 (mt)
REVERT: B  687 ARG cc_start: 0.7301 (ttt180) cc_final: 0.6719 (ptp90)
REVERT: B  709 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: B  725 ASP cc_start: 0.7169 (t0) cc_final: 0.6664 (m-30)
REVERT: B  742 GLU cc_start: 0.7745 (tp30) cc_final: 0.7375 (tt0)
REVERT: C   28 MET cc_start: 0.8660 (ptm) cc_final: 0.8244 (ttp)
REVERT: C   42 ASN cc_start: 0.7919 (m-40) cc_final: 0.7689 (m110)
REVERT: C   51 MET cc_start: 0.8898 (mmm) cc_final: 0.8483 (mmt)
REVERT: C   82 LYS cc_start: 0.3989 (OUTLIER) cc_final: 0.3707 (mtmm)
REVERT: C   83 ASP cc_start: 0.4261 (OUTLIER) cc_final: 0.3634 (t70)
REVERT: C  198 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6754 (mp)
REVERT: C  201 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7263 (tt)
  outliers start: 59
  outliers final: 18
  residues processed: 255
  average time/residue: 0.6553
  time to fit residues: 181.6889
Evaluate side-chains
  226 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  455 MET
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  268 GLN
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  514 VAL
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  213 ARG
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 111 optimal weight:    2.9990
   chunk 133 optimal weight:    0.0060
   chunk 167 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 114 optimal weight:    5.9990
   chunk 104 optimal weight:    1.9990
   chunk 102 optimal weight:    0.1980
   chunk 76 optimal weight:    0.0870
   chunk 158 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.4574

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A 505 HIS
B  47 HIS
B 124 GLN
B 314 ASN
B 690 GLN
C 182 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.131561 restraints weight = 21202.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.92
r_work: 0.3302 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14417  Z= 0.093
  Angle     :  0.473   7.144  19531  Z= 0.251
  Chirality :  0.038   0.157   2141
  Planarity :  0.004   0.044   2439
  Dihedral  : 10.554  75.946   2183
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.10 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.07 (0.20), residues: 1679
  helix:  1.30 (0.19), residues: 765
  sheet: -0.96 (0.38), residues: 170
  loop : -1.26 (0.21), residues: 744

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 151 
 TYR   0.020   0.001   TYR B 557 
 PHE   0.014   0.001   PHE C 168 
 TRP   0.026   0.001   TRP C  49 
 HIS   0.003   0.000   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (14417)
  covalent geometry    : angle       0.47312 (19531)
  hydrogen bonds       : bond        0.03448 (  666)
  hydrogen bonds       : angle       3.98217 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 213
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A   47 MET cc_start: 0.6040 (mtm) cc_final: 0.5748 (mtp)
REVERT: A   85 ASN cc_start: 0.8113 (m-40) cc_final: 0.7760 (m110)
REVERT: A   97 MET cc_start: 0.6927 (tmm) cc_final: 0.6461 (ttt)
REVERT: A  153 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6299 (mp0)
REVERT: A  203 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7265 (mm-30)
REVERT: A  304 MET cc_start: 0.8388 (mmm) cc_final: 0.8125 (tpt)
REVERT: A  544 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7732 (mm-30)
REVERT: A  568 ILE cc_start: 0.9130 (tp) cc_final: 0.8853 (pt)
REVERT: B  118 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8324 (mtt-85)
REVERT: B  287 LYS cc_start: 0.7703 (pptt) cc_final: 0.7052 (ptpt)
REVERT: B  669 LYS cc_start: 0.7939 (tttt) cc_final: 0.7563 (tptm)
REVERT: B  672 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7066 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7313 (mt)
REVERT: B  687 ARG cc_start: 0.7244 (ttt180) cc_final: 0.6689 (ptp90)
REVERT: B  725 ASP cc_start: 0.7180 (t0) cc_final: 0.6646 (m-30)
REVERT: B  742 GLU cc_start: 0.7698 (tp30) cc_final: 0.7326 (tt0)
REVERT: C    1 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5251 (mpp)
REVERT: C   40 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6809 (tt0)
REVERT: C   51 MET cc_start: 0.8941 (mmm) cc_final: 0.8497 (mmt)
REVERT: C   82 LYS cc_start: 0.3965 (OUTLIER) cc_final: 0.3657 (mtmt)
REVERT: C   83 ASP cc_start: 0.4227 (OUTLIER) cc_final: 0.3609 (t70)
REVERT: C  214 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6473 (mtm180)
  outliers start: 51
  outliers final: 16
  residues processed: 247
  average time/residue: 0.7058
  time to fit residues: 189.2963
Evaluate side-chains
  228 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 204
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  482 THR
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  214 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 135 optimal weight:    6.9990
   chunk 102 optimal weight:    8.9990
   chunk 98 optimal weight:    0.7980
   chunk 92 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 150 optimal weight:    0.0170
   chunk 106 optimal weight:    3.9990
   chunk 139 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    1.9622

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 268 GLN
B 314 ASN
B 452 ASN
B 690 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.158990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128504 restraints weight = 16990.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.52
r_work: 0.3266 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3161
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14417  Z= 0.154
  Angle     :  0.516   7.831  19531  Z= 0.274
  Chirality :  0.040   0.164   2141
  Planarity :  0.004   0.053   2439
  Dihedral  : 10.314  77.578   2165
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 16.90 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.19 (0.20), residues: 1679
  helix:  1.55 (0.19), residues: 774
  sheet: -0.87 (0.37), residues: 171
  loop : -1.20 (0.21), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 151 
 TYR   0.023   0.001   TYR B 557 
 PHE   0.015   0.001   PHE A 702 
 TRP   0.028   0.001   TRP C  49 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (14417)
  covalent geometry    : angle       0.51596 (19531)
  hydrogen bonds       : bond        0.04003 (  666)
  hydrogen bonds       : angle       4.01947 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 204
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.8193 (m-40) cc_final: 0.7844 (m110)
REVERT: A   97 MET cc_start: 0.7018 (tmm) cc_final: 0.6562 (ttt)
REVERT: A  304 MET cc_start: 0.8348 (mmm) cc_final: 0.8136 (tpt)
REVERT: A  455 MET cc_start: 0.8754 (ttt) cc_final: 0.7965 (mmm)
REVERT: A  683 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8162 (mp0)
REVERT: B  287 LYS cc_start: 0.7660 (pptt) cc_final: 0.7024 (ptpt)
REVERT: B  669 LYS cc_start: 0.7913 (tttt) cc_final: 0.7614 (tptm)
REVERT: B  672 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7111 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7831 (mm) cc_final: 0.7476 (mt)
REVERT: B  742 GLU cc_start: 0.7601 (tp30) cc_final: 0.7327 (tt0)
REVERT: C   40 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6780 (tt0)
REVERT: C   51 MET cc_start: 0.8940 (mmm) cc_final: 0.8511 (mmt)
REVERT: C   82 LYS cc_start: 0.4178 (OUTLIER) cc_final: 0.3860 (mtmt)
REVERT: C   83 ASP cc_start: 0.4326 (OUTLIER) cc_final: 0.3615 (t70)
REVERT: C  201 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7523 (tt)
  outliers start: 52
  outliers final: 31
  residues processed: 237
  average time/residue: 0.6704
  time to fit residues: 173.6231
Evaluate side-chains
  230 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  683 GLU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain B residue  744 THR
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 150 optimal weight:   40.0000
   chunk 65 optimal weight:    4.9990
   chunk 168 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 112 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    3.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 158 ASN
B 314 ASN
B 690 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.124364 restraints weight = 20131.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.88
r_work: 0.3197 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3074 r_free = 0.3074    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  14417  Z= 0.251
  Angle     :  0.607   7.056  19531  Z= 0.322
  Chirality :  0.044   0.195   2141
  Planarity :  0.005   0.041   2439
  Dihedral  : 10.475  79.064   2162
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 16.10 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -0.06 (0.20), residues: 1679
  helix:  1.20 (0.18), residues: 786
  sheet: -0.99 (0.38), residues: 167
  loop : -1.19 (0.22), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 151 
 TYR   0.026   0.002   TYR B 557 
 PHE   0.021   0.002   PHE A 702 
 TRP   0.029   0.002   TRP C  49 
 HIS   0.005   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (14417)
  covalent geometry    : angle       0.60711 (19531)
  hydrogen bonds       : bond        0.04868 (  666)
  hydrogen bonds       : angle       4.28003 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 196
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.7042 (tmm) cc_final: 0.6613 (ttt)
REVERT: A  455 MET cc_start: 0.8798 (ttt) cc_final: 0.8010 (mmm)
REVERT: B  169 ASP cc_start: 0.7806 (t0) cc_final: 0.7570 (t0)
REVERT: B  669 LYS cc_start: 0.7987 (tttt) cc_final: 0.7660 (tptm)
REVERT: B  672 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7031 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7544 (mt)
REVERT: B  742 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7442 (tt0)
REVERT: C   26 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7476 (t0)
REVERT: C   40 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6840 (tt0)
REVERT: C   51 MET cc_start: 0.8952 (mmm) cc_final: 0.8528 (mmt)
REVERT: C   82 LYS cc_start: 0.4258 (OUTLIER) cc_final: 0.3862 (mtmm)
REVERT: C  191 GLU cc_start: 0.7221 (tt0) cc_final: 0.6572 (mt-10)
REVERT: C  201 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7531 (tt)
  outliers start: 69
  outliers final: 34
  residues processed: 240
  average time/residue: 0.6765
  time to fit residues: 177.3034
Evaluate side-chains
  224 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLU
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  342 LEU
Chi-restraints excluded: chain A residue  367 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  290 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain B residue  742 GLU
Chi-restraints excluded: chain B residue  744 THR
Chi-restraints excluded: chain C residue   16 MET
Chi-restraints excluded: chain C residue   26 ASP
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  201 ILE
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 127 optimal weight:    3.9990
   chunk 13 optimal weight:    0.4980
   chunk 55 optimal weight:    5.9990
   chunk 150 optimal weight:    5.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 585 GLN
B 124 GLN
B 314 ASN
B 690 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132006 restraints weight = 19026.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.57
r_work: 0.3310 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14417  Z= 0.105
  Angle     :  0.487   8.292  19531  Z= 0.260
  Chirality :  0.038   0.161   2141
  Planarity :  0.003   0.038   2439
  Dihedral  : 10.214  76.653   2162
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.03 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.43 (0.20), residues: 1679
  helix:  1.71 (0.19), residues: 773
  sheet: -0.94 (0.38), residues: 175
  loop : -0.95 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 151 
 TYR   0.020   0.001   TYR B 557 
 PHE   0.014   0.001   PHE C 168 
 TRP   0.028   0.001   TRP C  49 
 HIS   0.003   0.000   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (14417)
  covalent geometry    : angle       0.48696 (19531)
  hydrogen bonds       : bond        0.03597 (  666)
  hydrogen bonds       : angle       4.01078 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.5758 (ptm) cc_final: 0.5405 (ppp)
REVERT: A   85 ASN cc_start: 0.8118 (m-40) cc_final: 0.7740 (m110)
REVERT: A   97 MET cc_start: 0.7026 (tmm) cc_final: 0.6596 (ttt)
REVERT: A  455 MET cc_start: 0.8784 (ttt) cc_final: 0.7989 (mmm)
REVERT: A  568 ILE cc_start: 0.9150 (tp) cc_final: 0.8860 (pt)
REVERT: A  611 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6916 (tp30)
REVERT: B  169 ASP cc_start: 0.7513 (t0) cc_final: 0.7298 (t0)
REVERT: B  287 LYS cc_start: 0.7617 (pptt) cc_final: 0.7044 (ptpt)
REVERT: B  669 LYS cc_start: 0.7900 (tttt) cc_final: 0.7583 (tptm)
REVERT: B  672 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7100 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7488 (mt)
REVERT: B  725 ASP cc_start: 0.7118 (t0) cc_final: 0.6612 (m-30)
REVERT: B  742 GLU cc_start: 0.7611 (tp30) cc_final: 0.7347 (tt0)
REVERT: C   40 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6732 (tt0)
REVERT: C   51 MET cc_start: 0.8828 (mmm) cc_final: 0.8387 (mmt)
REVERT: C   54 LYS cc_start: 0.7543 (mttt) cc_final: 0.7303 (mttp)
REVERT: C   82 LYS cc_start: 0.4247 (OUTLIER) cc_final: 0.3863 (mtmm)
REVERT: C   83 ASP cc_start: 0.4288 (OUTLIER) cc_final: 0.3643 (t70)
REVERT: C  191 GLU cc_start: 0.7090 (tt0) cc_final: 0.6518 (mt-10)
REVERT: C  214 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6641 (mtm180)
  outliers start: 35
  outliers final: 18
  residues processed: 236
  average time/residue: 0.6690
  time to fit residues: 171.7872
Evaluate side-chains
  219 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  611 GLU
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  214 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 17 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 131 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 132 optimal weight:    6.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 227 HIS
B 124 GLN
B 314 ASN
B 452 ASN
B 690 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.159308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.129568 restraints weight = 17001.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.54
r_work: 0.3253 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  14417  Z= 0.176
  Angle     :  0.537   7.228  19531  Z= 0.286
  Chirality :  0.041   0.177   2141
  Planarity :  0.004   0.051   2439
  Dihedral  : 10.257  78.753   2159
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.56 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.38 (0.20), residues: 1679
  helix:  1.59 (0.19), residues: 781
  sheet: -0.92 (0.39), residues: 169
  loop : -0.94 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 151 
 TYR   0.024   0.002   TYR B 557 
 PHE   0.021   0.002   PHE C 168 
 TRP   0.033   0.002   TRP C  49 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (14417)
  covalent geometry    : angle       0.53717 (19531)
  hydrogen bonds       : bond        0.04244 (  666)
  hydrogen bonds       : angle       4.10851 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 197
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.5642 (ptm) cc_final: 0.5268 (ppp)
REVERT: A   85 ASN cc_start: 0.8222 (m-40) cc_final: 0.7828 (m110)
REVERT: A   97 MET cc_start: 0.7075 (tmm) cc_final: 0.6594 (ttt)
REVERT: A  455 MET cc_start: 0.8804 (ttt) cc_final: 0.7995 (mmm)
REVERT: B  287 LYS cc_start: 0.7726 (pptt) cc_final: 0.7034 (ptpt)
REVERT: B  362 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7935 (mtm)
REVERT: B  669 LYS cc_start: 0.7894 (tttt) cc_final: 0.7550 (tptm)
REVERT: B  672 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7040 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (mt)
REVERT: B  742 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7364 (tt0)
REVERT: C   40 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6790 (tt0)
REVERT: C   51 MET cc_start: 0.8842 (mmm) cc_final: 0.8424 (mmt)
REVERT: C   54 LYS cc_start: 0.7565 (mttt) cc_final: 0.7307 (mttp)
REVERT: C   82 LYS cc_start: 0.4361 (OUTLIER) cc_final: 0.3294 (ptmm)
REVERT: C  191 GLU cc_start: 0.7115 (tt0) cc_final: 0.6528 (mt-10)
REVERT: C  214 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6649 (mtm180)
  outliers start: 50
  outliers final: 32
  residues processed: 230
  average time/residue: 0.6290
  time to fit residues: 158.0144
Evaluate side-chains
  230 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  362 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  517 ASN
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain B residue  742 GLU
Chi-restraints excluded: chain B residue  744 THR
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 124 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 148 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 136 optimal weight:    3.9990
   chunk 143 optimal weight:    4.9990
   chunk 154 optimal weight:    4.9990
   chunk 111 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 690 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.160334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.130404 restraints weight = 26071.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.08
r_work: 0.3217 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3062 r_free = 0.3062    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3062
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.2641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14417  Z= 0.145
  Angle     :  0.514   7.500  19531  Z= 0.274
  Chirality :  0.040   0.168   2141
  Planarity :  0.004   0.040   2439
  Dihedral  : 10.194  77.821   2159
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.36 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.44 (0.20), residues: 1679
  helix:  1.65 (0.19), residues: 779
  sheet: -0.90 (0.38), residues: 169
  loop : -0.89 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 151 
 TYR   0.022   0.001   TYR B 557 
 PHE   0.026   0.001   PHE A  46 
 TRP   0.034   0.001   TRP C  49 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (14417)
  covalent geometry    : angle       0.51444 (19531)
  hydrogen bonds       : bond        0.03972 (  666)
  hydrogen bonds       : angle       4.08140 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 202
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.5594 (ptm) cc_final: 0.5194 (ppp)
REVERT: A   85 ASN cc_start: 0.8188 (m-40) cc_final: 0.7783 (m110)
REVERT: A   97 MET cc_start: 0.7106 (tmm) cc_final: 0.6557 (ttt)
REVERT: A  455 MET cc_start: 0.8874 (ttt) cc_final: 0.8044 (mmm)
REVERT: B  287 LYS cc_start: 0.7718 (pptt) cc_final: 0.7061 (ptpt)
REVERT: B  362 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7975 (mtm)
REVERT: B  669 LYS cc_start: 0.7944 (tttt) cc_final: 0.7579 (tptm)
REVERT: B  672 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7034 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7505 (mt)
REVERT: B  725 ASP cc_start: 0.7218 (t0) cc_final: 0.6681 (m-30)
REVERT: B  742 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7436 (tt0)
REVERT: C    1 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5066 (mpp)
REVERT: C   40 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6848 (tt0)
REVERT: C   51 MET cc_start: 0.8852 (mmm) cc_final: 0.8434 (mmt)
REVERT: C   54 LYS cc_start: 0.7557 (mttt) cc_final: 0.7293 (mttp)
REVERT: C   82 LYS cc_start: 0.4231 (OUTLIER) cc_final: 0.3866 (mtmm)
REVERT: C  191 GLU cc_start: 0.7181 (tt0) cc_final: 0.6534 (mt-10)
REVERT: C  214 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6715 (mtm180)
  outliers start: 43
  outliers final: 27
  residues processed: 230
  average time/residue: 0.6866
  time to fit residues: 172.1921
Evaluate side-chains
  230 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 196
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  321 THR
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  362 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain B residue  517 ASN
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain B residue  742 GLU
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  214 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 59 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 690 GLN
C 127 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.162890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.133817 restraints weight = 18920.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.61
r_work: 0.3322 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3142
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3142 r_free = 0.3142    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3142
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14417  Z= 0.116
  Angle     :  0.486   7.755  19531  Z= 0.259
  Chirality :  0.039   0.163   2141
  Planarity :  0.003   0.040   2439
  Dihedral  : 10.087  77.298   2159
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 20.43 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.63 (0.21), residues: 1679
  helix:  1.82 (0.19), residues: 773
  sheet: -0.82 (0.39), residues: 169
  loop : -0.78 (0.22), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 175 
 TYR   0.021   0.001   TYR B 557 
 PHE   0.011   0.001   PHE A 702 
 TRP   0.035   0.001   TRP C  49 
 HIS   0.003   0.001   HIS C 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (14417)
  covalent geometry    : angle       0.48635 (19531)
  hydrogen bonds       : bond        0.03665 (  666)
  hydrogen bonds       : angle       3.99238 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 199
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 MET cc_start: 0.5600 (ptm) cc_final: 0.5209 (ppp)
REVERT: A   85 ASN cc_start: 0.8105 (m-40) cc_final: 0.7717 (m110)
REVERT: A   97 MET cc_start: 0.7056 (tmm) cc_final: 0.6573 (ttt)
REVERT: A  286 ASP cc_start: 0.8386 (m-30) cc_final: 0.8116 (m-30)
REVERT: A  455 MET cc_start: 0.8764 (ttt) cc_final: 0.7990 (mmm)
REVERT: B   69 ILE cc_start: 0.8418 (pt) cc_final: 0.8179 (pt)
REVERT: B  287 LYS cc_start: 0.7652 (pptt) cc_final: 0.7087 (ptpt)
REVERT: B  379 ARG cc_start: 0.8012 (ptm160) cc_final: 0.7803 (ptm160)
REVERT: B  669 LYS cc_start: 0.7865 (tttt) cc_final: 0.7589 (tptm)
REVERT: B  672 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7071 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7509 (mt)
REVERT: B  725 ASP cc_start: 0.7141 (t0) cc_final: 0.6624 (m-30)
REVERT: B  742 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7405 (tt0)
REVERT: C   40 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6739 (tt0)
REVERT: C   51 MET cc_start: 0.8824 (mmm) cc_final: 0.8372 (mmt)
REVERT: C   82 LYS cc_start: 0.4281 (OUTLIER) cc_final: 0.3917 (mtmm)
REVERT: C   83 ASP cc_start: 0.4351 (OUTLIER) cc_final: 0.3721 (t70)
REVERT: C  202 MET cc_start: 0.7973 (tpp) cc_final: 0.7763 (tpt)
REVERT: C  214 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6704 (mtm180)
  outliers start: 32
  outliers final: 25
  residues processed: 221
  average time/residue: 0.6798
  time to fit residues: 163.3856
Evaluate side-chains
  226 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  203 ARG
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain B residue  742 GLU
Chi-restraints excluded: chain B residue  744 THR
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  214 ARG
Chi-restraints excluded: chain C residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 160 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 146 optimal weight:    5.9990
   chunk 19 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 119 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    5.9990
   chunk 79 optimal weight:    8.9990
   chunk 76 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 452 ASN
B 597 ASN
B 690 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.162027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.131902 restraints weight = 19008.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.59
r_work: 0.3306 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3126 r_free = 0.3126    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3126
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14417  Z= 0.114
  Angle     :  0.489   8.659  19531  Z= 0.260
  Chirality :  0.039   0.158   2141
  Planarity :  0.003   0.039   2439
  Dihedral  :  9.991  77.271   2159
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.49 %
    Favored  : 77.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.65 (0.21), residues: 1679
  helix:  1.80 (0.19), residues: 780
  sheet: -0.79 (0.39), residues: 169
  loop : -0.76 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 175 
 TYR   0.021   0.001   TYR B 557 
 PHE   0.012   0.001   PHE B 412 
 TRP   0.033   0.001   TRP C  49 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (14417)
  covalent geometry    : angle       0.48924 (19531)
  hydrogen bonds       : bond        0.03626 (  666)
  hydrogen bonds       : angle       3.96541 ( 1882)

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

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

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3358 Ramachandran restraints generated.
    1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.6753 (ppp) cc_final: 0.6535 (pp-130)
REVERT: A   21 MET cc_start: 0.5584 (ptm) cc_final: 0.5184 (ppp)
REVERT: A   85 ASN cc_start: 0.8086 (m-40) cc_final: 0.7701 (m110)
REVERT: A   97 MET cc_start: 0.7040 (tmm) cc_final: 0.6582 (ttt)
REVERT: A  286 ASP cc_start: 0.8415 (m-30) cc_final: 0.8150 (m-30)
REVERT: A  455 MET cc_start: 0.8776 (ttt) cc_final: 0.7989 (mmm)
REVERT: B   69 ILE cc_start: 0.8402 (pt) cc_final: 0.8188 (pt)
REVERT: B  287 LYS cc_start: 0.7684 (pptt) cc_final: 0.7128 (ptpt)
REVERT: B  669 LYS cc_start: 0.7870 (tttt) cc_final: 0.7592 (tptm)
REVERT: B  672 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7085 (mtt-85)
REVERT: B  683 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7495 (mt)
REVERT: B  725 ASP cc_start: 0.7150 (t0) cc_final: 0.6633 (m-30)
REVERT: B  742 GLU cc_start: 0.7759 (tp30) cc_final: 0.7417 (tt0)
REVERT: C   40 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6735 (tt0)
REVERT: C   51 MET cc_start: 0.8837 (mmm) cc_final: 0.8387 (mmt)
REVERT: C   82 LYS cc_start: 0.4272 (OUTLIER) cc_final: 0.3913 (mtmm)
REVERT: C   83 ASP cc_start: 0.4272 (OUTLIER) cc_final: 0.3634 (t70)
REVERT: C  214 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6689 (mtm180)
  outliers start: 30
  outliers final: 24
  residues processed: 214
  average time/residue: 0.6410
  time to fit residues: 149.4462
Evaluate side-chains
  218 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 GLU
Chi-restraints excluded: chain A residue  251 GLU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  272 GLU
Chi-restraints excluded: chain A residue  323 ILE
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  612 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  148 GLU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  288 LYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  382 ASN
Chi-restraints excluded: chain B residue  392 ILE
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  683 LEU
Chi-restraints excluded: chain B residue  685 ASP
Chi-restraints excluded: chain B residue  704 THR
Chi-restraints excluded: chain C residue   40 GLU
Chi-restraints excluded: chain C residue   50 MET
Chi-restraints excluded: chain C residue   63 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   82 LYS
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue  203 VAL
Chi-restraints excluded: chain C residue  214 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 131 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 122 optimal weight:    6.9990
   chunk 157 optimal weight:   10.0000
   chunk 152 optimal weight:    4.9990
   chunk 144 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 71 optimal weight:    1.9990
   chunk 147 optimal weight:    0.4980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 124 GLN
B 452 ASN
B 690 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.160837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131071 restraints weight = 17056.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.50
r_work: 0.3282 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3118
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3118 r_free = 0.3118    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3118
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14417  Z= 0.140
  Angle     :  0.509   8.510  19531  Z= 0.270
  Chirality :  0.040   0.164   2141
  Planarity :  0.004   0.040   2439
  Dihedral  : 10.012  78.008   2159
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 20.29 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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:  0.65 (0.21), residues: 1679
  helix:  1.79 (0.19), residues: 776
  sheet: -0.81 (0.39), residues: 169
  loop : -0.72 (0.22), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 175 
 TYR   0.022   0.001   TYR B 557 
 PHE   0.013   0.001   PHE A 702 
 TRP   0.037   0.001   TRP C  49 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (14417)
  covalent geometry    : angle       0.50941 (19531)
  hydrogen bonds       : bond        0.03864 (  666)
  hydrogen bonds       : angle       4.01046 ( 1882)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5772.42 seconds
wall clock time: 98 minutes 56.63 seconds (5936.63 seconds total)