Starting phenix.real_space_refine
on Wed Mar  4 13:32:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avg_15682/03_2026/8avg_15682.cif"
  }
  resolution = 4.01
  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=   0.001
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
     Fe      4      7.16       5
     S      89      5.16       5
     C    8712      2.51       5
     N    2400      2.21       5
     O    2541      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 13746
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4720
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 25, 'TRANS': 577}
          Chain breaks: 9
    Chain: "B"
      Number of atoms: 5494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5494
          Classifications: {'peptide': 694}
          Link IDs: {'PTRANS': 28, 'TRANS': 665}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 3497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 3497
          Classifications: {'peptide': 435}
          Link IDs: {'PTRANS': 20, 'TRANS': 414}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'SF4': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10320  SG  CYS C  99      46.109  48.121  84.283  1.00 35.37           S
  ATOM  10421  SG  CYS C 112      51.785  48.553  81.278  1.00 47.71           S
  ATOM  10395  SG  CYS C 109      46.698  46.131  78.253  1.00 46.71           S

  Time building chain proxies: 2.89, per 1000 atoms: 0.21
  Number of scatterers: 13746
  At special positions: 0
  Unit cell: (79.98, 113.52, 156.52, 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)
     Fe      4     26.01
     S      89     16.00
     O    2541      8.00
     N    2400      7.00
     C    8712      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: 0.92
  Conformation dependent library (CDL) restraints added in 446.2 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 C 601 "
        pdb="FE4  SF4 C 601 " - pdb=" SG  CYS C 109 "
        pdb="FE1  SF4 C 601 " - pdb=" SG  CYS C  99 "
        pdb="FE2  SF4 C 601 " - pdb=" SG  CYS C 112 "
      Number of angles added : 9


  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3234

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 37 sheets defined
      11.7% alpha, 30.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 155 through 159
      removed outlier: 4.063A  pdb=" N   PHE A 158 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A 159 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 155 through 159'
    Processing helix  chain 'B' and resid 320 through 324
      removed outlier: 3.802A  pdb=" N   GLU B 323 " --> pdb=" O   PRO B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 481
      removed outlier: 4.246A  pdb=" N   VAL B 473 " --> pdb=" O   PRO B 469 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   GLU B 474 " --> pdb=" O   ARG B 470 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   ASN B 475 " --> pdb=" O   ASN B 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 554
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 3.956A  pdb=" N   SER C 103 " --> pdb=" O   PRO C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 131 through 141
    Processing helix  chain 'C' and resid 143 through 159
      removed outlier: 3.518A  pdb=" N   GLN C 147 " --> pdb=" O   ASP C 143 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY C 159 " --> pdb=" O   LEU C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 177
      removed outlier: 4.005A  pdb=" N   LEU C 177 " --> pdb=" O   PHE C 174 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 192
      removed outlier: 3.559A  pdb=" N   ARG C 182 " --> pdb=" O   PRO C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 209
    Processing helix  chain 'C' and resid 223 through 227
    Processing helix  chain 'C' and resid 228 through 239
    Processing helix  chain 'C' and resid 251 through 259
    Processing helix  chain 'C' and resid 264 through 276
      removed outlier: 3.549A  pdb=" N   CYS C 268 " --> pdb=" O   VAL C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 307
      removed outlier: 3.622A  pdb=" N   ILE C 298 " --> pdb=" O   LEU C 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 334
      removed outlier: 3.518A  pdb=" N   SER C 334 " --> pdb=" O   GLU C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 355
    Processing helix  chain 'C' and resid 382 through 395
      removed outlier: 3.636A  pdb=" N   LEU C 386 " --> pdb=" O   ASN C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 512
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
      removed outlier: 3.820A  pdb=" N   THR A 376 " --> pdb=" O   ASN A   3 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12
      removed outlier: 3.571A  pdb=" N   PHE A  12 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   TYR A 368 " --> pdb=" O   PHE A  12 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 27
      removed outlier: 3.929A  pdb=" N   CYS A  23 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 76
      removed outlier: 3.893A  pdb=" N   THR A  87 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASP A  91 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 117
      removed outlier: 7.013A  pdb=" N   ALA A 127 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   MET A 115 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   LEU A 125 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
      removed outlier: 5.215A  pdb=" N   TRP A 117 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   LEU A 123 " --> pdb=" O   TRP A 117 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 144 " --> pdb=" O   MET A 135 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   THR A 137 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   VAL A 142 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 200
    Processing sheet with id=AA7, first strand: chain 'A' and resid 245 through 246
      removed outlier: 4.108A  pdb=" N   ALA A 245 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 264 through 268
      removed outlier: 6.615A  pdb=" N   VAL A 265 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   HIS A 277 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   PHE A 267 " --> pdb=" O   HIS A 275 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 288 through 294
      removed outlier: 6.503A  pdb=" N   TRP A 304 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LEU A 292 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   ALA A 302 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 323 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   THR A 324 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   LEU A 332 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 378 through 379
      removed outlier: 4.449A  pdb=" N   ASP A 378 " --> pdb=" O   ALA A 392 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL A 399 " --> pdb=" O   ARG A 417 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   ARG A 417 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 401 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 424 through 429
      removed outlier: 6.567A  pdb=" N   LEU A 440 " --> pdb=" O   ASN A 425 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   VAL A 427 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   ALA A 438 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 510
    Processing sheet with id=AB4, first strand: chain 'A' and resid 519 through 520
    Processing sheet with id=AB5, first strand: chain 'A' and resid 558 through 561
      removed outlier: 6.682A  pdb=" N   GLN A 573 " --> pdb=" O   ILE A 559 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 572 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 579 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 610 through 616
      removed outlier: 4.055A  pdb=" N   ALA A 639 " --> pdb=" O   PHE A 631 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ILE A 633 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   GLU A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 645 through 648
      removed outlier: 3.614A  pdb=" N   ARG A 690 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 697 through 701
      removed outlier: 4.684A  pdb=" N   ILE A 709 " --> pdb=" O   VAL A 699 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 6 through 12
      removed outlier: 5.671A  pdb=" N   VAL B   8 " --> pdb=" O   ARG B 825 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ARG B 825 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL B 821 " --> pdb=" O   PHE B  12 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE B 812 " --> pdb=" O   TYR B 824 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   CYS B 815 " --> pdb=" O   ARG B 782 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ARG B 782 " --> pdb=" O   CYS B 815 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 23 through 24
    Processing sheet with id=AC2, first strand: chain 'B' and resid 61 through 66
      removed outlier: 6.499A  pdb=" N   GLY B  81 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   LEU B  64 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL B  79 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   TRP B  66 " --> pdb=" O   GLU B  77 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   GLU B  77 " --> pdb=" O   TRP B  66 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS B  99 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 113 through 117
      removed outlier: 3.550A  pdb=" N   ILE B 116 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA B 128 " --> pdb=" O   LYS B 144 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   VAL B 139 " --> pdb=" O   THR B 154 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   THR B 154 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ILE B 141 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU B 152 " --> pdb=" O   ILE B 141 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 164 through 169
      removed outlier: 4.719A  pdb=" N   CYS B 166 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLY B 181 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU B 178 " --> pdb=" O   TYR B 190 " (cutoff:3.500A)
      removed outlier: 6.117A  pdb=" N   ILE B 187 " --> pdb=" O   SER B 202 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   SER B 202 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   LEU B 189 " --> pdb=" O   ALA B 200 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 210 through 218
      removed outlier: 6.432A  pdb=" N   CYS B 227 " --> pdb=" O   ARG B 211 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   VAL B 213 " --> pdb=" O   ALA B 225 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA B 225 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   TRP B 215 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   PHE B 223 " --> pdb=" O   TRP B 215 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   THR B 217 " --> pdb=" O   ASP B 221 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ASP B 221 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 285 through 289
      removed outlier: 3.546A  pdb=" N   ALA B 287 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 294 through 296
    Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 318
      removed outlier: 3.562A  pdb=" N   LEU B 317 " --> pdb=" O   VAL B 331 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   VAL B 331 " --> pdb=" O   LEU B 317 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 343 through 348
      removed outlier: 6.295A  pdb=" N   HIS B 358 " --> pdb=" O   TYR B 344 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   CYS B 346 " --> pdb=" O   ILE B 356 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE B 356 " --> pdb=" O   CYS B 346 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   PHE B 348 " --> pdb=" O   MET B 354 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   MET B 354 " --> pdb=" O   PHE B 348 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 390 through 395
      removed outlier: 7.023A  pdb=" N   THR B 405 " --> pdb=" O   GLN B 391 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LEU B 393 " --> pdb=" O   ILE B 403 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   ILE B 403 " --> pdb=" O   LEU B 393 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU B 413 " --> pdb=" O   ILE B 433 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR B 429 " --> pdb=" O   TRP B 417 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 443 through 450
      removed outlier: 6.408A  pdb=" N   GLN B 453 " --> pdb=" O   ILE B 449 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 570 through 575
      removed outlier: 7.042A  pdb=" N   ALA B 585 " --> pdb=" O   VAL B 571 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   VAL B 573 " --> pdb=" O   ALA B 583 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   ALA B 583 " --> pdb=" O   VAL B 573 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 596 through 598
      removed outlier: 3.555A  pdb=" N   LEU B 598 " --> pdb=" O   GLN B 608 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   GLN B 608 " --> pdb=" O   LEU B 598 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 619 through 622
    Processing sheet with id=AD6, first strand: chain 'B' and resid 672 through 676
      removed outlier: 4.528A  pdb=" N   SER B 688 " --> pdb=" O   LYS B 692 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   LYS B 692 " --> pdb=" O   SER B 688 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL B 695 " --> pdb=" O   SER B 715 " (cutoff:3.500A)
      removed outlier: 4.880A  pdb=" N   SER B 715 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   GLY B 697 " --> pdb=" O   CYS B 713 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   CYS B 713 " --> pdb=" O   GLY B 697 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'B' and resid 723 through 728
      removed outlier: 6.495A  pdb=" N   GLY B 743 " --> pdb=" O   THR B 724 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   VAL B 726 " --> pdb=" O   ALA B 741 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA B 741 " --> pdb=" O   VAL B 726 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   VAL B 728 " --> pdb=" O   ILE B 739 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ILE B 739 " --> pdb=" O   VAL B 728 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'C' and resid 88 through 91
      removed outlier: 3.586A  pdb=" N   ALA C  88 " --> pdb=" O   LYS C 164 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLU C 166 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   VAL C 165 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   ILE C 218 " --> pdb=" O   VAL C 165 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   PHE C 167 " --> pdb=" O   ILE C 218 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE C 220 " --> pdb=" O   PHE C 167 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   ARG C 242 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE C 218 " --> pdb=" O   ARG C 242 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   GLU C 244 " --> pdb=" O   ILE C 218 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ILE C 220 " --> pdb=" O   GLU C 244 " (cutoff:3.500A)
      removed outlier: 8.433A  pdb=" N   GLY C 246 " --> pdb=" O   ILE C 220 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LYS C 280 " --> pdb=" O   ARG C 242 " (cutoff:3.500A)
      removed outlier: 5.651A  pdb=" N   GLU C 244 " --> pdb=" O   LYS C 280 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   VAL C 282 " --> pdb=" O   GLU C 244 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   GLY C 246 " --> pdb=" O   VAL C 282 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   HIS C 284 " --> pdb=" O   GLY C 246 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY C 314 " --> pdb=" O   VAL C 281 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   LEU C 317 " --> pdb=" O   TYR C 363 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'C' and resid 421 through 425
      removed outlier: 3.704A  pdb=" N   ALA C 429 " --> pdb=" O   GLY C 432 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'C' and resid 421 through 425
      removed outlier: 5.169A  pdb=" N   TRP C 433 " --> pdb=" O   LYS C 455 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   GLY C 449 " --> pdb=" O   TYR C 439 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASP C 441 " --> pdb=" O   LEU C 447 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   LEU C 447 " --> pdb=" O   ASP C 441 " (cutoff:3.500A)
      removed outlier: 8.363A  pdb=" N   ILE C 448 " --> pdb=" O   VAL C 477 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   VAL C 477 " --> pdb=" O   ILE C 448 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU C 450 " --> pdb=" O   LEU C 475 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   LEU C 475 " --> pdb=" O   LEU C 450 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   ARG C 452 " --> pdb=" O   ARG C 473 " (cutoff:3.500A)
      removed outlier: 5.879A  pdb=" N   SER C 470 " --> pdb=" O   ALA C 519 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   ILE C 521 " --> pdb=" O   SER C 470 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   VAL C 472 " --> pdb=" O   ILE C 521 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1008 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.41

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 5982
        1.43 -     1.64: 7956
        1.64 -     1.85: 117
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 14067
  Sorted by residual:
  bond pdb=" N   LYS A  20 "
       pdb=" CA  LYS A  20 "
    ideal  model  delta    sigma   weight residual
    1.452  1.490 -0.038 1.11e-02 8.12e+03 1.17e+01
  bond pdb=" N   ILE A  15 "
       pdb=" CA  ILE A  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.04e+00
  bond pdb=" N   VAL A  47 "
       pdb=" CA  VAL A  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.48e+00
  bond pdb=" N   ARG A  48 "
       pdb=" CA  ARG A  48 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.35e-02 5.49e+03 7.82e+00
  bond pdb=" N   GLN B 126 "
       pdb=" CA  GLN B 126 "
    ideal  model  delta    sigma   weight residual
    1.452  1.487 -0.035 1.25e-02 6.40e+03 7.76e+00
  ... (remaining 14062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 18214
        1.49 -     2.98: 727
        2.98 -     4.47: 128
        4.47 -     5.95: 25
        5.95 -     7.44: 4
  Bond angle restraints: 19098
  Sorted by residual:
  angle pdb=" C   PRO A  18 "
        pdb=" CA  PRO A  18 "
        pdb=" CB  PRO A  18 "
      ideal   model   delta    sigma   weight residual
     111.64  106.01    5.63 1.27e+00 6.20e-01 1.96e+01
  angle pdb=" N   PRO A  18 "
        pdb=" CA  PRO A  18 "
        pdb=" C   PRO A  18 "
      ideal   model   delta    sigma   weight residual
     111.26  117.97   -6.71 1.63e+00 3.76e-01 1.69e+01
  angle pdb=" N   HIS B 281 "
        pdb=" CA  HIS B 281 "
        pdb=" CB  HIS B 281 "
      ideal   model   delta    sigma   weight residual
     114.17  109.59    4.58 1.14e+00 7.69e-01 1.62e+01
  angle pdb=" CA  ARG A  49 "
        pdb=" C   ARG A  49 "
        pdb=" O   ARG A  49 "
      ideal   model   delta    sigma   weight residual
     122.44  117.24    5.20 1.32e+00 5.74e-01 1.55e+01
  angle pdb=" N   GLY B 105 "
        pdb=" CA  GLY B 105 "
        pdb=" C   GLY B 105 "
      ideal   model   delta    sigma   weight residual
     111.93  116.22   -4.29 1.15e+00 7.56e-01 1.39e+01
  ... (remaining 19093 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7443
       17.96 -    35.93: 726
       35.93 -    53.89: 115
       53.89 -    71.85: 31
       71.85 -    89.82: 20
  Dihedral angle restraints: 8335
    sinusoidal: 3341
      harmonic: 4994
  Sorted by residual:
  dihedral pdb=" CA  VAL A 510 "
           pdb=" C   VAL A 510 "
           pdb=" N   GLU A 511 "
           pdb=" CA  GLU A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.25  -29.75     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  CYS B 185 "
           pdb=" C   CYS B 185 "
           pdb=" N   ARG B 186 "
           pdb=" CA  ARG B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.77  -25.23     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  ASP A 513 "
           pdb=" C   ASP A 513 "
           pdb=" N   THR A 514 "
           pdb=" CA  THR A 514 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.81  -25.19     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 8332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1597
       0.048 -    0.096: 414
       0.096 -    0.144: 121
       0.144 -    0.192: 4
       0.192 -    0.240: 2
  Chirality restraints: 2138
  Sorted by residual:
  chirality pdb=" CA  SAM C 602 "
            pdb=" N   SAM C 602 "
            pdb=" C   SAM C 602 "
            pdb=" CB  SAM C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.69   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CA  ILE A  15 "
            pdb=" N   ILE A  15 "
            pdb=" C   ILE A  15 "
            pdb=" CB  ILE A  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.24e-01
  chirality pdb=" CA  VAL A 699 "
            pdb=" N   VAL A 699 "
            pdb=" C   VAL A 699 "
            pdb=" CB  VAL A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 2135 not shown)

  Planarity restraints: 2427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 236 "   -0.013 2.00e-02 2.50e+03   1.25e-02 3.92e+00
        pdb=" CG  TRP B 236 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 236 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 236 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 236 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 236 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 236 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 236 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 236 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 236 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 369 "    0.029 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO C 370 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C 370 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 370 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  20 "   -0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A  21 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2424 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 926
        2.73 -     3.27: 13490
        3.27 -     3.82: 21333
        3.82 -     4.36: 25000
        4.36 -     4.90: 44063
  Nonbonded interactions: 104812
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 248 "
            pdb=" NH1 ARG C 260 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" OG  SER A 118 "
            pdb=" OD1 ASP A 120 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ARG B 237 "
            pdb=" OG1 THR B 273 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OG1 THR A 609 "
            pdb=" OD1 ASP A 627 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OG1 THR A 128 "
            pdb=" OG1 THR A 132 "
     model   vdw
     2.207 3.040
  ... (remaining 104807 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.850
  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:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.580
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14070  Z= 0.186
  Angle     :  0.699   7.442  19107  Z= 0.413
  Chirality :  0.046   0.240   2138
  Planarity :  0.004   0.045   2427
  Dihedral  : 15.122  89.816   5101
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.34 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.66 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.19), residues: 1692
  helix: -0.24 (0.39), residues: 180
  sheet: -0.67 (0.23), residues: 535
  loop : -2.62 (0.18), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 697 
 TYR   0.013   0.001   TYR C 111 
 PHE   0.018   0.001   PHE A 228 
 TRP   0.033   0.001   TRP B 236 
 HIS   0.012   0.001   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14067)
  covalent geometry    : angle       0.69789 (19098)
  hydrogen bonds       : bond        0.16343 (  377)
  hydrogen bonds       : angle       7.31382 ( 1008)
  metal coordination   : bond        0.01315 (    3)
  metal coordination   : angle       2.17346 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 GLU cc_start: 0.8015 (tp30) cc_final: 0.7714 (tp30)
REVERT: C  434 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6459 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1022
  time to fit residues: 20.9509
Evaluate side-chains
  86 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0970
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A  30 GLN
A 231 GLN
A 659 HIS
** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 HIS
B 330 GLN
B 369 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 733 ASN
C 430 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.107513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.089522 restraints weight = 38216.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.090683 restraints weight = 34929.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.091080 restraints weight = 31477.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.091381 restraints weight = 21976.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.091630 restraints weight = 20062.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7269
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14070  Z= 0.105
  Angle     :  0.565   7.882  19107  Z= 0.296
  Chirality :  0.046   0.163   2138
  Planarity :  0.004   0.044   2427
  Dihedral  :  6.962  71.451   1894
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.45 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  5.13 %
    Favored  : 94.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.31 (0.20), residues: 1692
  helix:  0.03 (0.39), residues: 183
  sheet: -0.44 (0.23), residues: 535
  loop : -2.63 (0.18), residues: 974

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 260 
 TYR   0.016   0.001   TYR A 449 
 PHE   0.013   0.001   PHE B 684 
 TRP   0.018   0.001   TRP B 236 
 HIS   0.010   0.001   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (14067)
  covalent geometry    : angle       0.56025 (19098)
  hydrogen bonds       : bond        0.03426 (  377)
  hydrogen bonds       : angle       5.72686 ( 1008)
  metal coordination   : bond        0.01182 (    3)
  metal coordination   : angle       3.23727 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 GLU cc_start: 0.7870 (tp30) cc_final: 0.7573 (tp30)
REVERT: C  434 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6837 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1088
  time to fit residues: 22.8704
Evaluate side-chains
  89 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 135 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   chunk 155 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 51 optimal weight:    4.9990
   chunk 134 optimal weight:    0.7980
   chunk 80 optimal weight:    9.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 573 GLN
A 659 HIS
B 281 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 593 HIS
B 733 ASN
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.102346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.084660 restraints weight = 39185.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.084000 restraints weight = 36799.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.084821 restraints weight = 33347.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.085462 restraints weight = 22594.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.085838 restraints weight = 20100.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.164  14070  Z= 0.271
  Angle     :  0.730  12.150  19107  Z= 0.377
  Chirality :  0.051   0.211   2138
  Planarity :  0.005   0.048   2427
  Dihedral  :  7.614  77.776   1894
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 11.94 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  7.17 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.19), residues: 1692
  helix: -0.64 (0.37), residues: 182
  sheet: -0.63 (0.23), residues: 533
  loop : -2.90 (0.17), residues: 977

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 260 
 TYR   0.017   0.002   TYR C 181 
 PHE   0.019   0.002   PHE A 604 
 TRP   0.019   0.002   TRP A 509 
 HIS   0.012   0.002   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 (14067)
  covalent geometry    : angle       0.71248 (19098)
  hydrogen bonds       : bond        0.04873 (  377)
  hydrogen bonds       : angle       6.13750 ( 1008)
  metal coordination   : bond        0.02291 (    3)
  metal coordination   : angle       7.25815 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 TYR cc_start: 0.6775 (m-80) cc_final: 0.6563 (m-80)
REVERT: C  135 MET cc_start: 0.6938 (pmm) cc_final: 0.6712 (pmm)
REVERT: C  347 GLU cc_start: 0.8047 (tp30) cc_final: 0.7702 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1092
  time to fit residues: 18.6640
Evaluate side-chains
  75 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 133 optimal weight:    0.0980
   chunk 156 optimal weight:    0.3980
   chunk 131 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 123 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 163 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 634 ASN
A 659 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.106882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.088583 restraints weight = 38470.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.090698 restraints weight = 40762.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.091247 restraints weight = 25582.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.091460 restraints weight = 20221.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.091778 restraints weight = 19355.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14070  Z= 0.110
  Angle     :  0.589  10.526  19107  Z= 0.304
  Chirality :  0.046   0.154   2138
  Planarity :  0.004   0.049   2427
  Dihedral  :  6.717  66.391   1894
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.22 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  3.42 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.20), residues: 1692
  helix: -0.23 (0.39), residues: 183
  sheet: -0.51 (0.23), residues: 542
  loop : -2.70 (0.18), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 260 
 TYR   0.012   0.001   TYR C 181 
 PHE   0.017   0.001   PHE A 515 
 TRP   0.016   0.001   TRP B 236 
 HIS   0.012   0.001   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (14067)
  covalent geometry    : angle       0.57799 (19098)
  hydrogen bonds       : bond        0.03334 (  377)
  hydrogen bonds       : angle       5.59122 ( 1008)
  metal coordination   : bond        0.01250 (    3)
  metal coordination   : angle       5.22248 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 GLU cc_start: 0.7897 (tp30) cc_final: 0.7567 (tp30)
REVERT: C  382 ASN cc_start: 0.7767 (p0) cc_final: 0.7405 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1109
  time to fit residues: 22.0309
Evaluate side-chains
  82 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 149 optimal weight:    1.9990
   chunk 161 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 171 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 48 optimal weight:    7.9990
   chunk 141 optimal weight:    3.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
A 435 ASN
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 HIS
A 659 HIS
B 281 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 150 HIS
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.105904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.088029 restraints weight = 38757.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.088475 restraints weight = 39903.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.089118 restraints weight = 36181.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.089557 restraints weight = 24394.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.089824 restraints weight = 22335.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  14070  Z= 0.135
  Angle     :  0.595  11.241  19107  Z= 0.307
  Chirality :  0.047   0.153   2138
  Planarity :  0.004   0.044   2427
  Dihedral  :  6.550  65.526   1894
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.63 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.22 %
    Favored  : 96.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.19), residues: 1692
  helix: -0.22 (0.38), residues: 182
  sheet: -0.46 (0.23), residues: 531
  loop : -2.70 (0.18), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 260 
 TYR   0.018   0.001   TYR A 449 
 PHE   0.012   0.001   PHE A 207 
 TRP   0.016   0.001   TRP B 236 
 HIS   0.012   0.001   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (14067)
  covalent geometry    : angle       0.58164 (19098)
  hydrogen bonds       : bond        0.03461 (  377)
  hydrogen bonds       : angle       5.57628 ( 1008)
  metal coordination   : bond        0.01379 (    3)
  metal coordination   : angle       5.78491 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  319 TYR cc_start: 0.6715 (m-80) cc_final: 0.6470 (m-80)
REVERT: C  135 MET cc_start: 0.6974 (pmm) cc_final: 0.6638 (pmm)
REVERT: C  347 GLU cc_start: 0.7995 (tp30) cc_final: 0.7679 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1165
  time to fit residues: 21.9126
Evaluate side-chains
  79 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 154 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 144 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 145 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 170 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0270
   chunk 104 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 435 ASN
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
B 281 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
C 150 HIS
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 430 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.106527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.087991 restraints weight = 38535.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.089510 restraints weight = 39287.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.089976 restraints weight = 27657.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091059 restraints weight = 21071.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.091104 restraints weight = 18177.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14070  Z= 0.107
  Angle     :  0.565  11.178  19107  Z= 0.293
  Chirality :  0.046   0.143   2138
  Planarity :  0.004   0.045   2427
  Dihedral  :  6.269  60.725   1894
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.57 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.50 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.20), residues: 1692
  helix: -0.05 (0.39), residues: 183
  sheet: -0.40 (0.23), residues: 545
  loop : -2.59 (0.18), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 260 
 TYR   0.012   0.001   TYR C 181 
 PHE   0.013   0.001   PHE B 684 
 TRP   0.019   0.001   TRP B 236 
 HIS   0.004   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (14067)
  covalent geometry    : angle       0.55314 (19098)
  hydrogen bonds       : bond        0.03124 (  377)
  hydrogen bonds       : angle       5.33998 ( 1008)
  metal coordination   : bond        0.01126 (    3)
  metal coordination   : angle       5.40926 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  561 LEU cc_start: 0.7927 (tp) cc_final: 0.7690 (pp)
REVERT: C  347 GLU cc_start: 0.7832 (tp30) cc_final: 0.7494 (tp30)
  outliers start: 1
  outliers final: 1
  residues processed: 127
  average time/residue: 0.1083
  time to fit residues: 20.9541
Evaluate side-chains
  84 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 75 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 140 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 161 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 160 optimal weight:    0.9980
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.9320

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

Flipped N/Q/H residues before XYZ refinement:
A  16 GLN
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 HIS
A 659 HIS
B 281 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.106326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.088077 restraints weight = 38637.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.089447 restraints weight = 40755.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.089909 restraints weight = 29738.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.090912 restraints weight = 23157.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.091001 restraints weight = 20405.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  14070  Z= 0.124
  Angle     :  0.593  11.413  19107  Z= 0.302
  Chirality :  0.046   0.152   2138
  Planarity :  0.004   0.044   2427
  Dihedral  :  6.290  61.254   1894
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  9.69 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.63 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.20), residues: 1692
  helix: -0.12 (0.38), residues: 184
  sheet: -0.53 (0.23), residues: 557
  loop : -2.62 (0.18), residues: 951

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 260 
 TYR   0.012   0.001   TYR C 181 
 PHE   0.013   0.001   PHE A 207 
 TRP   0.020   0.001   TRP B 236 
 HIS   0.005   0.001   HIS A 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (14067)
  covalent geometry    : angle       0.57986 (19098)
  hydrogen bonds       : bond        0.03364 (  377)
  hydrogen bonds       : angle       5.35762 ( 1008)
  metal coordination   : bond        0.01263 (    3)
  metal coordination   : angle       5.83728 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 GLU cc_start: 0.7865 (tp30) cc_final: 0.7544 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1103
  time to fit residues: 20.3051
Evaluate side-chains
  86 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 165 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0980
   chunk 43 optimal weight:    9.9990
   chunk 170 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.104504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.086396 restraints weight = 38755.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.087209 restraints weight = 41055.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.087804 restraints weight = 34459.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.088117 restraints weight = 24141.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.088458 restraints weight = 22282.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098  14070  Z= 0.181
  Angle     :  0.669  12.498  19107  Z= 0.338
  Chirality :  0.048   0.179   2138
  Planarity :  0.005   0.045   2427
  Dihedral  :  6.710  66.614   1894
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.34 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.19), residues: 1692
  helix: -0.41 (0.37), residues: 183
  sheet: -0.67 (0.23), residues: 553
  loop : -2.68 (0.18), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 260 
 TYR   0.015   0.002   TYR C 181 
 PHE   0.015   0.002   PHE A 207 
 TRP   0.020   0.001   TRP B 236 
 HIS   0.006   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (14067)
  covalent geometry    : angle       0.64697 (19098)
  hydrogen bonds       : bond        0.03978 (  377)
  hydrogen bonds       : angle       5.57690 ( 1008)
  metal coordination   : bond        0.01709 (    3)
  metal coordination   : angle       7.84481 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8123 (mmp) cc_final: 0.7861 (mmt)
REVERT: A  319 TYR cc_start: 0.6662 (m-80) cc_final: 0.6431 (m-80)
REVERT: C  135 MET cc_start: 0.6971 (pmm) cc_final: 0.6759 (pmm)
REVERT: C  382 ASN cc_start: 0.7506 (p0) cc_final: 0.7306 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1008
  time to fit residues: 17.5909
Evaluate side-chains
  77 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 167 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 164 optimal weight:    0.7980
   chunk 44 optimal weight:   10.0000
   chunk 148 optimal weight:    0.9990
   chunk 102 optimal weight:    3.9990
   chunk 144 optimal weight:    0.9980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
B 281 HIS
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 590 GLN
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.106501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.088466 restraints weight = 38777.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.090048 restraints weight = 41529.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.090685 restraints weight = 28448.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.091313 restraints weight = 21123.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.091535 restraints weight = 20065.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14070  Z= 0.116
  Angle     :  0.610  12.070  19107  Z= 0.307
  Chirality :  0.047   0.168   2138
  Planarity :  0.004   0.045   2427
  Dihedral  :  6.372  61.047   1894
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.81 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.38 (0.20), residues: 1692
  helix: -0.26 (0.38), residues: 184
  sheet: -0.53 (0.23), residues: 550
  loop : -2.61 (0.18), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 260 
 TYR   0.011   0.001   TYR C 181 
 PHE   0.014   0.001   PHE B 685 
 TRP   0.021   0.001   TRP B 236 
 HIS   0.004   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (14067)
  covalent geometry    : angle       0.59417 (19098)
  hydrogen bonds       : bond        0.03285 (  377)
  hydrogen bonds       : angle       5.31947 ( 1008)
  metal coordination   : bond        0.01318 (    3)
  metal coordination   : angle       6.46357 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: 0.7802 (tmm) cc_final: 0.7590 (tmm)
REVERT: C  135 MET cc_start: 0.6940 (pmm) cc_final: 0.6727 (pmm)
REVERT: C  347 GLU cc_start: 0.8173 (tp30) cc_final: 0.7789 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1008
  time to fit residues: 18.8933
Evaluate side-chains
  84 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 150 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 111 optimal weight:    0.3980
   chunk 92 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 171 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 530 HIS
A 545 GLN
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.104646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.086647 restraints weight = 38643.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.087306 restraints weight = 38887.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.087961 restraints weight = 30412.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.088114 restraints weight = 22601.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.088471 restraints weight = 21284.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  14070  Z= 0.168
  Angle     :  0.659  13.162  19107  Z= 0.330
  Chirality :  0.048   0.183   2138
  Planarity :  0.005   0.062   2427
  Dihedral  :  6.614  65.394   1894
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.82 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.19), residues: 1692
  helix: -0.45 (0.37), residues: 184
  sheet: -0.62 (0.23), residues: 552
  loop : -2.68 (0.18), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.016   0.001   TYR C 181 
 PHE   0.014   0.002   PHE A 207 
 TRP   0.021   0.001   TRP B 236 
 HIS   0.006   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (14067)
  covalent geometry    : angle       0.63603 (19098)
  hydrogen bonds       : bond        0.03839 (  377)
  hydrogen bonds       : angle       5.50449 ( 1008)
  metal coordination   : bond        0.01616 (    3)
  metal coordination   : angle       7.92746 (    9)

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

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

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3384 Ramachandran restraints generated.
    1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8287 (mmp) cc_final: 0.7900 (mmt)
REVERT: A  319 TYR cc_start: 0.6630 (m-80) cc_final: 0.6415 (m-80)
REVERT: B  393 LEU cc_start: 0.7972 (pt) cc_final: 0.7748 (pt)
REVERT: C  135 MET cc_start: 0.7055 (pmm) cc_final: 0.6827 (pmm)
REVERT: C  347 GLU cc_start: 0.8235 (tp30) cc_final: 0.7834 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0969
  time to fit residues: 16.5324
Evaluate side-chains
  78 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 172
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 142 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 170 optimal weight:    0.6980
   chunk 129 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 128 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 125 optimal weight:    6.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 330 GLN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.103950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.086059 restraints weight = 39014.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.087397 restraints weight = 41123.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.087768 restraints weight = 30635.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.088846 restraints weight = 22307.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.088861 restraints weight = 18803.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  14070  Z= 0.189
  Angle     :  0.691  14.384  19107  Z= 0.346
  Chirality :  0.049   0.174   2138
  Planarity :  0.005   0.045   2427
  Dihedral  :  6.855  67.623   1894
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.93 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.63 (0.19), residues: 1692
  helix: -0.56 (0.37), residues: 184
  sheet: -0.73 (0.23), residues: 552
  loop : -2.74 (0.18), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 260 
 TYR   0.029   0.002   TYR B 344 
 PHE   0.016   0.002   PHE B 472 
 TRP   0.017   0.002   TRP B  90 
 HIS   0.006   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (14067)
  covalent geometry    : angle       0.66349 (19098)
  hydrogen bonds       : bond        0.04007 (  377)
  hydrogen bonds       : angle       5.68373 ( 1008)
  metal coordination   : bond        0.01745 (    3)
  metal coordination   : angle       8.92596 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1809.71 seconds
wall clock time: 32 minutes 21.79 seconds (1941.79 seconds total)