Starting phenix.real_space_refine
on Sat Aug 23 01:58:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hf4_34712/08_2025/8hf4_34712.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      30      5.16       5
     C    5732      2.51       5
     N    1462      2.21       5
     O    1686      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8916
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "B"
      Number of atoms: 4427
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 563, 4427
          Classifications: {'peptide': 563}
          Link IDs: {'PTRANS': 12, 'TRANS': 550}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'AGS': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.26
  Number of scatterers: 8916
  At special positions: 0
  Unit cell: (82.368, 81.51, 140.712, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       6     15.00
     O    1686      8.00
     N    1462      7.00
     C    5732      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: 0.84
  Conformation dependent library (CDL) restraints added in 236.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 4 sheets defined
      70.4% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 157 through 164
      removed outlier: 3.511A  pdb=" N   VAL A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LYS A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 195
      removed outlier: 3.574A  pdb=" N   ILE A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 189 " --> pdb=" O   GLY A 185 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLN A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   SER A 191 " --> pdb=" O   TYR A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 250
      removed outlier: 3.720A  pdb=" N   ASP A 240 " --> pdb=" O   ARG A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 4.038A  pdb=" N   PHE A 257 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ALA A 258 " --> pdb=" O   MET A 254 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   THR A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ARG A 260 " --> pdb=" O   PHE A 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 253 through 260'
    Processing helix  chain 'A' and resid 261 through 276
      removed outlier: 3.663A  pdb=" N   ILE A 265 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   SER A 274 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ILE A 275 " --> pdb=" O   ASP A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 279
      No H-bonds generated for 'chain 'A' and resid 277 through 279'
    Processing helix  chain 'A' and resid 280 through 288
      removed outlier: 3.742A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 304
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 3.640A  pdb=" N   MET A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 325
      removed outlier: 3.979A  pdb=" N   ILE A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   PHE A 325 " --> pdb=" O   ILE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 353
      removed outlier: 3.671A  pdb=" N   PHE A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLU A 330 " --> pdb=" O   MET A 326 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 331 " --> pdb=" O   LYS A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
    Processing helix  chain 'A' and resid 362 through 416
      removed outlier: 4.021A  pdb=" N   ARG A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 459
      removed outlier: 3.544A  pdb=" N   TYR A 433 " --> pdb=" O   THR A 429 " (cutoff:3.500A)
      Proline residue:  A 437  - end of helix
      removed outlier: 3.733A  pdb=" N   ILE A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   THR A 446 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   LYS A 447 " --> pdb=" O   ASN A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 464
      removed outlier: 3.603A  pdb=" N   LEU A 463 " --> pdb=" O   GLU A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 531
      removed outlier: 3.658A  pdb=" N   VAL A 531 " --> pdb=" O   ALA A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 559
      removed outlier: 3.501A  pdb=" N   LEU A 556 " --> pdb=" O   ASP A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 580
    Processing helix  chain 'A' and resid 588 through 598
    Processing helix  chain 'A' and resid 623 through 638
      removed outlier: 3.834A  pdb=" N   THR A 638 " --> pdb=" O   ARG A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 666
      removed outlier: 3.927A  pdb=" N   ALA A 666 " --> pdb=" O   ASP A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 683
      removed outlier: 4.390A  pdb=" N   ALA A 681 " --> pdb=" O   ARG A 677 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ARG A 683 " --> pdb=" O   THR A 679 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 677 through 683'
    Processing helix  chain 'A' and resid 700 through 706
    Processing helix  chain 'A' and resid 709 through 717
    Processing helix  chain 'B' and resid 157 through 163
      removed outlier: 3.979A  pdb=" N   LYS B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 195
      removed outlier: 3.533A  pdb=" N   ASN B 170 " --> pdb=" O   GLY B 166 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE B 183 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B 184 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY B 185 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 189 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   SER B 191 " --> pdb=" O   TYR B 187 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE B 192 " --> pdb=" O   TYR B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 203 through 251
      removed outlier: 3.702A  pdb=" N   ILE B 207 " --> pdb=" O   SER B 203 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 208 " --> pdb=" O   THR B 204 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   SER B 209 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE B 210 " --> pdb=" O   GLY B 206 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLY B 211 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP B 240 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   HIS B 251 " --> pdb=" O   LYS B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 260
      removed outlier: 4.041A  pdb=" N   PHE B 257 " --> pdb=" O   PRO B 253 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA B 258 " --> pdb=" O   MET B 254 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG B 260 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 260'
    Processing helix  chain 'B' and resid 261 through 276
      removed outlier: 3.633A  pdb=" N   ILE B 265 " --> pdb=" O   ARG B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 304
      removed outlier: 3.815A  pdb=" N   ILE B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 299 " --> pdb=" O   ILE B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 312
    Processing helix  chain 'B' and resid 313 through 325
      removed outlier: 4.019A  pdb=" N   ILE B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   PHE B 325 " --> pdb=" O   ILE B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 353
      removed outlier: 3.894A  pdb=" N   PHE B 329 " --> pdb=" O   PHE B 325 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLU B 330 " --> pdb=" O   MET B 326 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS B 331 " --> pdb=" O   LYS B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 360
    Processing helix  chain 'B' and resid 362 through 417
      removed outlier: 4.002A  pdb=" N   ARG B 366 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLN B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 459
      removed outlier: 3.978A  pdb=" N   VAL B 432 " --> pdb=" O   ASN B 428 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   TYR B 433 " --> pdb=" O   THR B 429 " (cutoff:3.500A)
      Proline residue:  B 437  - end of helix
      removed outlier: 4.056A  pdb=" N   THR B 446 " --> pdb=" O   ILE B 442 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   LYS B 447 " --> pdb=" O   ASN B 443 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 454 " --> pdb=" O   THR B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 522 through 531
    Processing helix  chain 'B' and resid 549 through 551
      No H-bonds generated for 'chain 'B' and resid 549 through 551'
    Processing helix  chain 'B' and resid 552 through 559
    Processing helix  chain 'B' and resid 573 through 579
    Processing helix  chain 'B' and resid 588 through 598
    Processing helix  chain 'B' and resid 602 through 607
    Processing helix  chain 'B' and resid 623 through 638
      removed outlier: 3.702A  pdb=" N   THR B 638 " --> pdb=" O   ARG B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 666
      removed outlier: 3.829A  pdb=" N   ALA B 666 " --> pdb=" O   ASP B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 684
      removed outlier: 3.787A  pdb=" N   GLU B 682 " --> pdb=" O   LEU B 678 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ARG B 683 " --> pdb=" O   THR B 679 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   THR B 684 " --> pdb=" O   ILE B 680 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 678 through 684'
    Processing helix  chain 'B' and resid 700 through 708
      removed outlier: 3.589A  pdb=" N   LEU B 704 " --> pdb=" O   LYS B 700 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY B 708 " --> pdb=" O   LEU B 704 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 717
    Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503
      removed outlier: 4.062A  pdb=" N   LEU A 500 " --> pdb=" O   TYR A 491 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   VAL A 489 " --> pdb=" O   ASP A 502 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER A 542 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LYS A 487 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU A 540 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   VAL A 489 " --> pdb=" O   GLN A 538 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   GLN A 538 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 562
      removed outlier: 6.577A  pdb=" N   ASN A 561 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   ASP A 646 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL A 513 " --> pdb=" O   PHE A 673 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   LYS A 512 " --> pdb=" O   LYS A 686 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   VAL A 688 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ALA A 514 " --> pdb=" O   VAL A 688 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   LEU A 690 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   VAL A 516 " --> pdb=" O   LEU A 690 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 699 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU A 697 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 504 through 505
      removed outlier: 3.792A  pdb=" N   LEU B 505 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   PHE B 486 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   SER B 542 " --> pdb=" O   PHE B 486 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   GLN B 488 " --> pdb=" O   GLU B 540 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   GLU B 540 " --> pdb=" O   GLN B 488 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN B 538 " --> pdb=" O   HIS B 490 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 563
      removed outlier: 6.795A  pdb=" N   ASN B 561 " --> pdb=" O   ILE B 644 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE B 643 " --> pdb=" O   ILE B 672 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   ILE B 674 " --> pdb=" O   ILE B 643 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU B 645 " --> pdb=" O   ILE B 674 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL B 513 " --> pdb=" O   PHE B 673 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   VAL B 688 " --> pdb=" O   LYS B 512 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ALA B 514 " --> pdb=" O   VAL B 688 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   LEU B 690 " --> pdb=" O   ALA B 514 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL B 516 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLU B 697 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1575 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.50

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.19 -     1.37: 2896
        1.37 -     1.54: 6074
        1.54 -     1.72: 22
        1.72 -     1.89: 56
        1.89 -     2.07: 2
  Bond restraints: 9050
  Sorted by residual:
  bond pdb=" C4  AGS A 801 "
       pdb=" C5  AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.458 -0.072 1.00e-02 1.00e+04 5.25e+01
  bond pdb=" C4  AGS B 801 "
       pdb=" C5  AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.386  1.458 -0.072 1.00e-02 1.00e+04 5.21e+01
  bond pdb=" PG  AGS A 801 "
       pdb=" S1G AGS A 801 "
    ideal  model  delta    sigma   weight residual
    1.949  2.070 -0.121 2.00e-02 2.50e+03 3.63e+01
  bond pdb=" PG  AGS B 801 "
       pdb=" S1G AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.949  2.069 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C5  AGS B 801 "
       pdb=" C6  AGS B 801 "
    ideal  model  delta    sigma   weight residual
    1.409  1.469 -0.060 1.00e-02 1.00e+04 3.61e+01
  ... (remaining 9045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 11918
        1.89 -     3.78: 260
        3.78 -     5.67: 72
        5.67 -     7.56: 12
        7.56 -     9.45: 16
  Bond angle restraints: 12278
  Sorted by residual:
  angle pdb=" C5  AGS A 801 "
        pdb=" C4  AGS A 801 "
        pdb=" N3  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     126.80  118.84    7.96 7.41e-01 1.82e+00 1.16e+02
  angle pdb=" C5  AGS B 801 "
        pdb=" C4  AGS B 801 "
        pdb=" N3  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     126.80  118.87    7.93 7.41e-01 1.82e+00 1.15e+02
  angle pdb=" C4  AGS B 801 "
        pdb=" C5  AGS B 801 "
        pdb=" N7  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     110.73  106.97    3.76 4.52e-01 4.89e+00 6.92e+01
  angle pdb=" C5  AGS B 801 "
        pdb=" N7  AGS B 801 "
        pdb=" C8  AGS B 801 "
      ideal   model   delta    sigma   weight residual
     103.67  107.21   -3.54 4.26e-01 5.51e+00 6.92e+01
  angle pdb=" C4  AGS A 801 "
        pdb=" C5  AGS A 801 "
        pdb=" N7  AGS A 801 "
      ideal   model   delta    sigma   weight residual
     110.73  106.97    3.76 4.52e-01 4.89e+00 6.91e+01
  ... (remaining 12273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.82: 5110
       23.82 -    47.64: 347
       47.64 -    71.46: 20
       71.46 -    95.27: 11
       95.27 -   119.09: 2
  Dihedral angle restraints: 5490
    sinusoidal: 2196
      harmonic: 3294
  Sorted by residual:
  dihedral pdb=" C   PHE B 673 "
           pdb=" N   PHE B 673 "
           pdb=" CA  PHE B 673 "
           pdb=" CB  PHE B 673 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.61  -10.99     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" O1A AGS A 801 "
           pdb=" O3A AGS A 801 "
           pdb=" PA  AGS A 801 "
           pdb=" PB  AGS A 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   51.36 -119.09     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" O1A AGS B 801 "
           pdb=" O3A AGS B 801 "
           pdb=" PA  AGS B 801 "
           pdb=" PB  AGS B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   51.35 -119.08     1      3.00e+01 1.11e-03 1.59e+01
  ... (remaining 5487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1387
       0.076 -    0.151: 89
       0.151 -    0.227: 19
       0.227 -    0.302: 3
       0.302 -    0.378: 4
  Chirality restraints: 1502
  Sorted by residual:
  chirality pdb=" CA  SER B 519 "
            pdb=" N   SER B 519 "
            pdb=" C   SER B 519 "
            pdb=" CB  SER B 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  LYS B 528 "
            pdb=" N   LYS B 528 "
            pdb=" C   LYS B 528 "
            pdb=" CB  LYS B 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.78e+00
  chirality pdb=" CB  ILE A 600 "
            pdb=" CA  ILE A 600 "
            pdb=" CG1 ILE A 600 "
            pdb=" CG2 ILE A 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.66e+00
  ... (remaining 1499 not shown)

  Planarity restraints: 1522
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 187 "    0.016 2.00e-02 2.50e+03   3.23e-02 1.04e+01
        pdb=" C   TYR B 187 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR B 187 "    0.021 2.00e-02 2.50e+03
        pdb=" N   TYR B 188 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 563 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO B 564 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO B 564 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 564 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 436 "   -0.035 5.00e-02 4.00e+02   5.30e-02 4.50e+00
        pdb=" N   PRO B 437 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 437 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 437 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1519 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1015
        2.75 -     3.28: 9189
        3.28 -     3.82: 14353
        3.82 -     4.36: 15601
        4.36 -     4.90: 27944
  Nonbonded interactions: 68102
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 653 "
            pdb=" OG1 THR B 656 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR A 524 "
            pdb=" O2G AGS A 801 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OG1 THR B 175 "
            pdb=" OE1 GLN B 226 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   SER B 519 "
            pdb=" O1B AGS B 801 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ILE B 207 "
            pdb=" N   SER B 209 "
     model   vdw
     2.293 3.120
  ... (remaining 68097 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.680
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
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      :  0.006   0.121   9050  Z= 0.428
  Angle     :  0.755   9.449  12278  Z= 0.509
  Chirality :  0.048   0.378   1502
  Planarity :  0.004   0.054   1522
  Dihedral  : 14.956 119.092   3366
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.72 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  1.41 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.09 %
  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 aren not related in a simple way.
  whole:  2.04 (0.26), residues: 1122
  helix:  2.75 (0.20), residues: 686
  sheet:  1.12 (0.69), residues: 72
  loop : -1.50 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 677 
 TYR   0.013   0.001   TYR B 562 
 PHE   0.030   0.001   PHE B 673 
 TRP   0.009   0.001   TRP A 408 
 HIS   0.002   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 9050)
  covalent geometry    : angle       0.75483 (12278)
  hydrogen bonds       : bond        0.17133 (  532)
  hydrogen bonds       : angle       4.96679 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  683 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mtp85)
REVERT: B  198 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7904 (Cg_endo)
REVERT: B  529 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8610 (mtt)
  outliers start: 11
  outliers final: 1
  residues processed: 99
  average time/residue: 0.4913
  time to fit residues: 52.8857
Evaluate side-chains
  56 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain B residue  529 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 566 GLN
** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 365 GLN
B 566 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.086106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065700 restraints weight = 21989.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.27
r_work: 0.3015 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9050  Z= 0.156
  Angle     :  0.576  10.270  12278  Z= 0.300
  Chirality :  0.041   0.364   1502
  Planarity :  0.003   0.041   1522
  Dihedral  :  8.058 142.477   1261
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.80 %
    Favored  : 88.08 %
  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 aren not related in a simple way.
  whole:  2.07 (0.26), residues: 1122
  helix:  2.74 (0.20), residues: 704
  sheet:  0.67 (0.64), residues: 78
  loop : -1.55 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 677 
 TYR   0.019   0.001   TYR A 559 
 PHE   0.010   0.001   PHE A 673 
 TRP   0.005   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 9050)
  covalent geometry    : angle       0.57551 (12278)
  hydrogen bonds       : bond        0.07380 (  532)
  hydrogen bonds       : angle       3.98664 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  193 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8110 (mp)
REVERT: A  201 MET cc_start: 0.8522 (mtp) cc_final: 0.8281 (mpp)
REVERT: A  409 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8208 (tpp)
REVERT: A  676 HIS cc_start: 0.8936 (m170) cc_final: 0.8666 (m-70)
REVERT: B  201 MET cc_start: 0.6728 (mmm) cc_final: 0.6059 (mmm)
REVERT: B  458 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: B  599 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7158 (tm-30)
  outliers start: 21
  outliers final: 7
  residues processed: 74
  average time/residue: 0.4518
  time to fit residues: 36.6952
Evaluate side-chains
  59 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 ILE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  676 HIS
Chi-restraints excluded: chain B residue  713 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN
B 488 GLN
B 504 ASN
B 538 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.085935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.065439 restraints weight = 21717.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.25
r_work: 0.3014 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9050  Z= 0.139
  Angle     :  0.531  10.386  12278  Z= 0.273
  Chirality :  0.039   0.277   1502
  Planarity :  0.003   0.039   1522
  Dihedral  :  8.154 142.786   1252
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.64 %
    Favored  : 84.55 %
  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 aren not related in a simple way.
  whole:  2.14 (0.26), residues: 1122
  helix:  2.80 (0.20), residues: 702
  sheet:  0.47 (0.63), residues: 80
  loop : -1.47 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 677 
 TYR   0.014   0.001   TYR B 187 
 PHE   0.013   0.001   PHE B 250 
 TRP   0.008   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9050)
  covalent geometry    : angle       0.53123 (12278)
  hydrogen bonds       : bond        0.07061 (  532)
  hydrogen bonds       : angle       3.78698 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  201 MET cc_start: 0.8407 (mtp) cc_final: 0.8203 (mpp)
REVERT: A  326 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8316 (ptp)
REVERT: A  604 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8501 (pt)
REVERT: A  676 HIS cc_start: 0.8955 (m170) cc_final: 0.8706 (m-70)
REVERT: B  201 MET cc_start: 0.7429 (mmm) cc_final: 0.6887 (mmm)
REVERT: B  419 MET cc_start: 0.8171 (ptm) cc_final: 0.7694 (ptm)
REVERT: B  599 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7190 (tm-30)
  outliers start: 18
  outliers final: 5
  residues processed: 69
  average time/residue: 0.4355
  time to fit residues: 33.0975
Evaluate side-chains
  58 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 76 optimal weight:    0.1980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN
B 538 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.086104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065566 restraints weight = 22040.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.28
r_work: 0.3012 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9050  Z= 0.130
  Angle     :  0.511   7.451  12278  Z= 0.264
  Chirality :  0.038   0.201   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.078 143.503   1252
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.95 %
    Favored  : 82.63 %
  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 aren not related in a simple way.
  whole:  2.27 (0.26), residues: 1122
  helix:  2.93 (0.19), residues: 702
  sheet:  0.45 (0.63), residues: 80
  loop : -1.48 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 202 
 TYR   0.012   0.001   TYR B 187 
 PHE   0.007   0.001   PHE A 673 
 TRP   0.007   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9050)
  covalent geometry    : angle       0.51061 (12278)
  hydrogen bonds       : bond        0.06747 (  532)
  hydrogen bonds       : angle       3.61490 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (ptp)
REVERT: A  676 HIS cc_start: 0.8968 (m170) cc_final: 0.8727 (m-70)
REVERT: B  201 MET cc_start: 0.7792 (mmm) cc_final: 0.7094 (mmm)
REVERT: B  599 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7226 (tm-30)
REVERT: B  622 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.6956 (tp)
  outliers start: 24
  outliers final: 10
  residues processed: 72
  average time/residue: 0.4027
  time to fit residues: 32.1507
Evaluate side-chains
  65 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  622 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN
B 538 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.086641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066494 restraints weight = 21755.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 3.22
r_work: 0.3036 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9050  Z= 0.120
  Angle     :  0.502   8.763  12278  Z= 0.257
  Chirality :  0.038   0.182   1502
  Planarity :  0.003   0.035   1522
  Dihedral  :  8.033 143.381   1252
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.66 %
    Favored  : 81.52 %
  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 aren not related in a simple way.
  whole:  2.33 (0.26), residues: 1122
  helix:  2.98 (0.20), residues: 702
  sheet:  0.40 (0.63), residues: 80
  loop : -1.45 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 202 
 TYR   0.011   0.001   TYR A 559 
 PHE   0.006   0.001   PHE A 673 
 TRP   0.005   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9050)
  covalent geometry    : angle       0.50170 (12278)
  hydrogen bonds       : bond        0.06355 (  532)
  hydrogen bonds       : angle       3.49690 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  326 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8366 (ptp)
REVERT: A  484 MET cc_start: 0.8693 (ttm) cc_final: 0.8462 (ttm)
REVERT: A  676 HIS cc_start: 0.8966 (m170) cc_final: 0.8722 (m-70)
REVERT: B  201 MET cc_start: 0.7856 (mmm) cc_final: 0.7079 (mmm)
REVERT: B  419 MET cc_start: 0.7712 (ptm) cc_final: 0.7371 (ptm)
REVERT: B  599 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7164 (tm-30)
REVERT: B  622 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6702 (tp)
  outliers start: 28
  outliers final: 17
  residues processed: 74
  average time/residue: 0.4327
  time to fit residues: 35.2591
Evaluate side-chains
  69 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  192 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.085898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.065393 restraints weight = 21989.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 3.28
r_work: 0.3010 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9050  Z= 0.130
  Angle     :  0.503   7.705  12278  Z= 0.258
  Chirality :  0.037   0.185   1502
  Planarity :  0.003   0.033   1522
  Dihedral  :  8.019 144.637   1252
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 16.57 %
    Favored  : 80.61 %
  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 aren not related in a simple way.
  whole:  2.33 (0.26), residues: 1122
  helix:  3.00 (0.20), residues: 702
  sheet:  0.34 (0.63), residues: 80
  loop : -1.48 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 677 
 TYR   0.010   0.001   TYR B 187 
 PHE   0.006   0.001   PHE B 250 
 TRP   0.006   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9050)
  covalent geometry    : angle       0.50320 (12278)
  hydrogen bonds       : bond        0.06592 (  532)
  hydrogen bonds       : angle       3.50504 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: A  326 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8334 (ptp)
REVERT: A  676 HIS cc_start: 0.8964 (m170) cc_final: 0.8727 (m-70)
REVERT: B  201 MET cc_start: 0.7997 (mmm) cc_final: 0.7296 (mtp)
REVERT: B  676 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8527 (t70)
  outliers start: 28
  outliers final: 16
  residues processed: 74
  average time/residue: 0.4266
  time to fit residues: 34.7794
Evaluate side-chains
  67 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  326 MET
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  368 GLN
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 100 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 3 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.082340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.061835 restraints weight = 22182.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 3.23
r_work: 0.2934 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9050  Z= 0.173
  Angle     :  0.563   9.300  12278  Z= 0.291
  Chirality :  0.039   0.194   1502
  Planarity :  0.003   0.034   1522
  Dihedral  :  8.192 151.229   1252
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.98 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.26), residues: 1122
  helix:  2.80 (0.19), residues: 702
  sheet:  0.21 (0.63), residues: 80
  loop : -1.50 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 606 
 TYR   0.017   0.001   TYR B 187 
 PHE   0.008   0.001   PHE B 250 
 TRP   0.004   0.001   TRP A 408 
 HIS   0.004   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9050)
  covalent geometry    : angle       0.56348 (12278)
  hydrogen bonds       : bond        0.07812 (  532)
  hydrogen bonds       : angle       3.76759 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  350 ASP cc_start: 0.8872 (t0) cc_final: 0.8550 (m-30)
REVERT: A  484 MET cc_start: 0.8775 (ttm) cc_final: 0.8562 (ttm)
REVERT: B  201 MET cc_start: 0.8295 (mmm) cc_final: 0.7729 (mtp)
REVERT: B  368 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7232 (mp10)
  outliers start: 26
  outliers final: 17
  residues processed: 69
  average time/residue: 0.4460
  time to fit residues: 33.6908
Evaluate side-chains
  66 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  368 GLN
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.083875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.063445 restraints weight = 21848.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 3.23
r_work: 0.2971 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.135
  Angle     :  0.528   8.550  12278  Z= 0.270
  Chirality :  0.038   0.198   1502
  Planarity :  0.003   0.038   1522
  Dihedral  :  8.201 152.443   1252
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.59 %
    Favored  : 79.09 %
  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 aren not related in a simple way.
  whole:  2.20 (0.26), residues: 1122
  helix:  2.90 (0.19), residues: 702
  sheet:  0.22 (0.63), residues: 80
  loop : -1.51 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 677 
 TYR   0.010   0.001   TYR B 187 
 PHE   0.007   0.001   PHE A 673 
 TRP   0.006   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9050)
  covalent geometry    : angle       0.52792 (12278)
  hydrogen bonds       : bond        0.07172 (  532)
  hydrogen bonds       : angle       3.63157 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 50
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 ASP cc_start: 0.8836 (t0) cc_final: 0.8531 (m-30)
REVERT: B  201 MET cc_start: 0.8386 (mmm) cc_final: 0.7758 (mtp)
REVERT: B  676 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8487 (t70)
  outliers start: 23
  outliers final: 16
  residues processed: 67
  average time/residue: 0.4325
  time to fit residues: 32.1734
Evaluate side-chains
  66 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  368 GLN
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 15 optimal weight:    0.0270
   chunk 92 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.3844

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

Flipped N/Q/H residues before XYZ refinement:
B 538 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.084142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.063775 restraints weight = 21782.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.20
r_work: 0.2979 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.135
  Angle     :  0.524   8.633  12278  Z= 0.269
  Chirality :  0.038   0.231   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.165 152.634   1252
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 19.09 %
    Favored  : 78.79 %
  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 aren not related in a simple way.
  whole:  2.21 (0.26), residues: 1122
  helix:  2.91 (0.19), residues: 702
  sheet:  0.20 (0.63), residues: 80
  loop : -1.49 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 677 
 TYR   0.009   0.001   TYR B 187 
 PHE   0.006   0.001   PHE A 673 
 TRP   0.007   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9050)
  covalent geometry    : angle       0.52370 (12278)
  hydrogen bonds       : bond        0.07010 (  532)
  hydrogen bonds       : angle       3.59566 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 48
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 ASP cc_start: 0.8843 (t0) cc_final: 0.8467 (m-30)
REVERT: B  201 MET cc_start: 0.8439 (mmm) cc_final: 0.7827 (mtp)
REVERT: B  676 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8520 (t70)
  outliers start: 21
  outliers final: 19
  residues processed: 63
  average time/residue: 0.4455
  time to fit residues: 31.0201
Evaluate side-chains
  65 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 45
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  368 GLN
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 68 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9990
   chunk 110 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.084454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.064058 restraints weight = 21766.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.21
r_work: 0.2985 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9050  Z= 0.132
  Angle     :  0.528   9.096  12278  Z= 0.269
  Chirality :  0.038   0.246   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.153 153.116   1252
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.39 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.26), residues: 1122
  helix:  2.91 (0.19), residues: 704
  sheet:  0.20 (0.63), residues: 80
  loop : -1.53 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 677 
 TYR   0.009   0.001   TYR B 187 
 PHE   0.006   0.001   PHE A 673 
 TRP   0.011   0.001   TRP A 408 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9050)
  covalent geometry    : angle       0.52808 (12278)
  hydrogen bonds       : bond        0.06886 (  532)
  hydrogen bonds       : angle       3.56101 ( 1575)

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

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

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2244 Ramachandran restraints generated.
    1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  350 ASP cc_start: 0.8818 (t0) cc_final: 0.8457 (m-30)
REVERT: B  201 MET cc_start: 0.8469 (mmm) cc_final: 0.7778 (mtp)
REVERT: B  676 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (t70)
  outliers start: 20
  outliers final: 19
  residues processed: 64
  average time/residue: 0.4500
  time to fit residues: 31.7885
Evaluate side-chains
  68 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 48
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  188 TYR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  250 PHE
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  604 ILE
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  642 VAL
Chi-restraints excluded: chain B residue  177 LEU
Chi-restraints excluded: chain B residue  188 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  275 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  368 GLN
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  676 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.085588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.065375 restraints weight = 21599.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 3.22
r_work: 0.3009 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   9050  Z= 0.124
  Angle     :  0.525   8.670  12278  Z= 0.268
  Chirality :  0.038   0.321   1502
  Planarity :  0.003   0.037   1522
  Dihedral  :  8.108 152.918   1252
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 19.39 %
    Favored  : 78.69 %
  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 aren not related in a simple way.
  whole:  2.24 (0.26), residues: 1122
  helix:  2.92 (0.20), residues: 704
  sheet:  0.26 (0.63), residues: 80
  loop : -1.49 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 601 
 TYR   0.008   0.001   TYR A 427 
 PHE   0.006   0.001   PHE A 673 
 TRP   0.002   0.001   TRP A 408 
 HIS   0.003   0.001   HIS B 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 9050)
  covalent geometry    : angle       0.52520 (12278)
  hydrogen bonds       : bond        0.06489 (  532)
  hydrogen bonds       : angle       3.51366 ( 1575)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2511.83 seconds
wall clock time: 43 minutes 53.27 seconds (2633.27 seconds total)