Starting phenix.real_space_refine
on Wed Mar  4 13:49:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aib_11794/03_2026/7aib_11794.map"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      41      5.16       5
     C    8493      2.51       5
     N    2500      2.21       5
     O    2739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 13839
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 661, 5206
          Classifications: {'peptide': 661}
          Link IDs: {'PTRANS': 27, 'TRANS': 633}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5225
          Classifications: {'peptide': 663}
          Link IDs: {'PTRANS': 27, 'TRANS': 635}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2116
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 9, 'TRANS': 257}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 621
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "E"
      Number of atoms: 609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 609
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.12, per 1000 atoms: 0.23
  Number of scatterers: 13839
  At special positions: 0
  Unit cell: (133.76, 110.88, 130.24, 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      41     16.00
     P      66     15.00
     O    2739      8.00
     N    2500      7.00
     C    8493      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.22
  Conformation dependent library (CDL) restraints added in 450.7 milliseconds
  

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2980

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      51.7% alpha, 13.8% beta
      30 base pairs and 58 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 162 through 174
      removed outlier: 3.562A  pdb=" N   MET A 166 " --> pdb=" O   ASP A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 190
      removed outlier: 3.601A  pdb=" N   LEU A 189 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 204
    Processing helix  chain 'A' and resid 205 through 218
    Processing helix  chain 'A' and resid 222 through 226
      removed outlier: 3.507A  pdb=" N   PHE A 225 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 248
      removed outlier: 4.110A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   CYS A 246 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.774A  pdb=" N   ARG A 274 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 296
      removed outlier: 3.648A  pdb=" N   VAL A 294 " --> pdb=" O   THR A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 313
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 334 through 343
      removed outlier: 3.516A  pdb=" N   LEU A 338 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.514A  pdb=" N   ILE A 351 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 373
    Processing helix  chain 'A' and resid 374 through 382
    Processing helix  chain 'A' and resid 387 through 398
    Processing helix  chain 'A' and resid 400 through 411
    Processing helix  chain 'A' and resid 430 through 442
      removed outlier: 3.755A  pdb=" N   ALA A 440 " --> pdb=" O   TRP A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 4.579A  pdb=" N   HIS A 483 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 479 through 483'
    Processing helix  chain 'A' and resid 503 through 536
      removed outlier: 3.865A  pdb=" N   PHE A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP A 533 " --> pdb=" O   GLU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 565
    Processing helix  chain 'A' and resid 587 through 592
    Processing helix  chain 'A' and resid 619 through 635
    Processing helix  chain 'A' and resid 673 through 684
      removed outlier: 3.560A  pdb=" N   ASN A 679 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 718
      removed outlier: 3.960A  pdb=" N   GLY A 704 " --> pdb=" O   SER A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 735
    Processing helix  chain 'A' and resid 771 through 779
      removed outlier: 3.941A  pdb=" N   ALA A 777 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU A 778 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 797
      removed outlier: 3.546A  pdb=" N   ILE A 786 " --> pdb=" O   PRO A 782 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLU A 795 " --> pdb=" O   GLN A 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 174
      removed outlier: 3.561A  pdb=" N   MET B 166 " --> pdb=" O   ASP B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 190
      removed outlier: 3.606A  pdb=" N   LEU B 189 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 204
    Processing helix  chain 'B' and resid 205 through 218
    Processing helix  chain 'B' and resid 222 through 226
    Processing helix  chain 'B' and resid 230 through 248
      removed outlier: 4.092A  pdb=" N   ALA B 236 " --> pdb=" O   ARG B 232 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   CYS B 246 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 277
      removed outlier: 3.515A  pdb=" N   ARG B 274 " --> pdb=" O   ASP B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 296
      removed outlier: 3.629A  pdb=" N   VAL B 294 " --> pdb=" O   THR B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 313
    Processing helix  chain 'B' and resid 317 through 343
      removed outlier: 4.991A  pdb=" N   ASP B 333 " --> pdb=" O   GLY B 329 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   PHE B 334 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ALA B 336 " --> pdb=" O   GLN B 332 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   GLY B 337 " --> pdb=" O   ASP B 333 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 338 " --> pdb=" O   PHE B 334 " (cutoff:3.500A)
      Proline residue:  B 340  - end of helix
    Processing helix  chain 'B' and resid 347 through 357
    Processing helix  chain 'B' and resid 361 through 373
    Processing helix  chain 'B' and resid 374 through 382
    Processing helix  chain 'B' and resid 387 through 398
      removed outlier: 3.573A  pdb=" N   GLY B 398 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 411
    Processing helix  chain 'B' and resid 430 through 442
      removed outlier: 3.732A  pdb=" N   ALA B 440 " --> pdb=" O   TRP B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 459
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 4.559A  pdb=" N   HIS B 483 " --> pdb=" O   ARG B 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 479 through 483'
    Processing helix  chain 'B' and resid 503 through 536
      removed outlier: 3.615A  pdb=" N   ASP B 511 " --> pdb=" O   LYS B 507 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS B 512 " --> pdb=" O   GLU B 508 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLY B 518 " --> pdb=" O   LEU B 514 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   PHE B 532 " --> pdb=" O   TYR B 528 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASP B 533 " --> pdb=" O   GLU B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 566
    Processing helix  chain 'B' and resid 587 through 592
    Processing helix  chain 'B' and resid 619 through 635
    Processing helix  chain 'B' and resid 672 through 684
      removed outlier: 3.586A  pdb=" N   GLU B 676 " --> pdb=" O   VAL B 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 718
      removed outlier: 3.516A  pdb=" N   SER B 706 " --> pdb=" O   TYR B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 729 through 735
    Processing helix  chain 'B' and resid 771 through 779
      removed outlier: 3.923A  pdb=" N   ALA B 777 " --> pdb=" O   LEU B 773 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU B 778 " --> pdb=" O   ALA B 774 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 797
      removed outlier: 3.802A  pdb=" N   GLU B 795 " --> pdb=" O   GLN B 791 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 37
      removed outlier: 3.661A  pdb=" N   VAL C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 73
      removed outlier: 3.919A  pdb=" N   ALA C  69 " --> pdb=" O   LYS C  65 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LEU C  70 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   LEU C  72 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 103
    Processing helix  chain 'C' and resid 155 through 161
      removed outlier: 3.541A  pdb=" N   LYS C 159 " --> pdb=" O   PRO C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 182
    Processing helix  chain 'C' and resid 208 through 223
      removed outlier: 6.792A  pdb=" N   THR C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 9.120A  pdb=" N   ALA C 219 " --> pdb=" O   ILE C 215 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE C 220 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU C 221 " --> pdb=" O   GLY C 217 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN C 223 " --> pdb=" O   ALA C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 246
      removed outlier: 3.559A  pdb=" N   THR C 246 " --> pdb=" O   PRO C 243 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 243 through 246'
    Processing helix  chain 'C' and resid 249 through 252
      removed outlier: 3.632A  pdb=" N   GLU C 252 " --> pdb=" O   ALA C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 249 through 252'
    Processing helix  chain 'C' and resid 265 through 276
      removed outlier: 4.052A  pdb=" N   ASN C 269 " --> pdb=" O   ASP C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 316 through 331
      removed outlier: 3.781A  pdb=" N   SER C 328 " --> pdb=" O   GLN C 324 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL C 329 " --> pdb=" O   GLY C 325 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN C 331 " --> pdb=" O   LEU C 327 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 158
      removed outlier: 3.531A  pdb=" N   ARG A 156 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR A 147 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA A 181 " --> pdb=" O   ILE A 136 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   GLN A 138 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   LEU A 178 " --> pdb=" O   ARG A 197 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ARG A 199 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   TYR A 180 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269
      removed outlier: 6.420A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 653 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   THR A 655 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ARG A 652 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
      removed outlier: 7.395A  pdb=" N   LEU A 691 " --> pdb=" O   ARG A 652 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   PHE A 654 " --> pdb=" O   LEU A 691 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   ASP A 693 " --> pdb=" O   PHE A 654 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU A 610 " --> pdb=" O   PHE A 725 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   MET A 609 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   VAL A 745 " --> pdb=" O   MET A 609 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   ILE A 611 " --> pdb=" O   VAL A 745 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   LEU A 747 " --> pdb=" O   ILE A 611 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   THR A 613 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
      removed outlier: 8.252A  pdb=" N   ALA A 749 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASP A 748 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   SER A 761 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   LEU A 750 " --> pdb=" O   MET A 759 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET A 759 " --> pdb=" O   LEU A 750 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   HIS A 752 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ALA A 757 " --> pdb=" O   HIS A 752 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466
      removed outlier: 5.882A  pdb=" N   ILE A 502 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ARG A 491 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 572
      removed outlier: 5.944A  pdb=" N   THR A 571 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   THR A 581 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   LEU A 601 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 196 through 199
      removed outlier: 6.495A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ARG B 199 " --> pdb=" O   LEU B 178 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   TYR B 180 " --> pdb=" O   ARG B 199 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   ALA B 181 " --> pdb=" O   ILE B 136 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   GLN B 138 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG B 156 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 268 through 269
      removed outlier: 7.090A  pdb=" N   ILE B 268 " --> pdb=" O   ILE B 653 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   THR B 655 " --> pdb=" O   ILE B 268 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU B 610 " --> pdb=" O   PHE B 725 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   MET B 609 " --> pdb=" O   ALA B 743 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   VAL B 745 " --> pdb=" O   MET B 609 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE B 611 " --> pdb=" O   VAL B 745 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   LEU B 747 " --> pdb=" O   ILE B 611 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   THR B 613 " --> pdb=" O   LEU B 747 " (cutoff:3.500A)
      removed outlier: 8.523A  pdb=" N   ALA B 749 " --> pdb=" O   THR B 613 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   SER B 761 " --> pdb=" O   ASP B 748 " (cutoff:3.500A)
      removed outlier: 8.234A  pdb=" N   LEU B 750 " --> pdb=" O   MET B 759 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   MET B 759 " --> pdb=" O   LEU B 750 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   HIS B 752 " --> pdb=" O   ALA B 757 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA B 757 " --> pdb=" O   HIS B 752 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 464 through 466
      removed outlier: 5.902A  pdb=" N   ILE B 502 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   ARG B 491 " --> pdb=" O   ILE B 502 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 572
      removed outlier: 5.896A  pdb=" N   THR B 571 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   THR B 581 " --> pdb=" O   LEU B 601 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU B 601 " --> pdb=" O   THR B 581 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 135 through 136
      removed outlier: 4.139A  pdb=" N   THR C 143 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE C  42 " --> pdb=" O   ASN C 188 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   SER C 190 " --> pdb=" O   ILE C  42 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   ILE C  44 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   HIS C 191 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 4.941A  pdb=" N   ILE C 195 " --> pdb=" O   HIS C 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 224 through 231
      removed outlier: 3.507A  pdb=" N   LEU C 290 " --> pdb=" O   TYR C 255 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ARG C 261 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)

    623 hydrogen bonds defined for protein.
    1776 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      76 hydrogen bonds
      152 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      58 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.61 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2240
        1.31 -     1.44: 3805
        1.44 -     1.57: 7941
        1.57 -     1.70: 128
        1.70 -     1.83: 80
  Bond restraints: 14194
  Sorted by residual:
  bond pdb=" N3B ANP B1801 "
       pdb=" PG  ANP B1801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.632  0.163 2.00e-02 2.50e+03 6.63e+01
  bond pdb=" N3B ANP A1801 "
       pdb=" PG  ANP A1801 "
    ideal  model  delta    sigma   weight residual
    1.795  1.634  0.161 2.00e-02 2.50e+03 6.47e+01
  bond pdb=" CE1 HIS A 682 "
       pdb=" NE2 HIS A 682 "
    ideal  model  delta    sigma   weight residual
    1.321  1.373 -0.052 1.00e-02 1.00e+04 2.75e+01
  bond pdb=" N   ILE A 503 "
       pdb=" CA  ILE A 503 "
    ideal  model  delta    sigma   weight residual
    1.462  1.506 -0.044 8.70e-03 1.32e+04 2.57e+01
  bond pdb=" O3A ANP B1801 "
       pdb=" PB  ANP B1801 "
    ideal  model  delta    sigma   weight residual
    1.700  1.603  0.097 2.00e-02 2.50e+03 2.35e+01
  ... (remaining 14189 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 15867
        2.43 -     4.86: 3294
        4.86 -     7.30: 295
        7.30 -     9.73: 21
        9.73 -    12.16: 3
  Bond angle restraints: 19480
  Sorted by residual:
  angle pdb=" C   PHE A 143 "
        pdb=" N   GLY A 144 "
        pdb=" CA  GLY A 144 "
      ideal   model   delta    sigma   weight residual
     121.65  127.06   -5.41 6.80e-01 2.16e+00 6.32e+01
  angle pdb=" N   LEU C 150 "
        pdb=" CA  LEU C 150 "
        pdb=" C   LEU C 150 "
      ideal   model   delta    sigma   weight residual
     111.07  102.93    8.14 1.07e+00 8.73e-01 5.78e+01
  angle pdb=" N   ASP A 265 "
        pdb=" CA  ASP A 265 "
        pdb=" C   ASP A 265 "
      ideal   model   delta    sigma   weight residual
     111.33  103.23    8.10 1.21e+00 6.83e-01 4.48e+01
  angle pdb=" N   ILE A 695 "
        pdb=" CA  ILE A 695 "
        pdb=" C   ILE A 695 "
      ideal   model   delta    sigma   weight residual
     109.37  100.49    8.88 1.35e+00 5.49e-01 4.32e+01
  angle pdb=" C   PHE B 143 "
        pdb=" N   GLY B 144 "
        pdb=" CA  GLY B 144 "
      ideal   model   delta    sigma   weight residual
     121.65  126.09   -4.44 6.80e-01 2.16e+00 4.26e+01
  ... (remaining 19475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.66: 7876
       31.66 -    63.31: 603
       63.31 -    94.97: 48
       94.97 -   126.63: 0
      126.63 -   158.28: 2
  Dihedral angle restraints: 8529
    sinusoidal: 3918
      harmonic: 4611
  Sorted by residual:
  dihedral pdb=" N   TYR C 152 "
           pdb=" C   TYR C 152 "
           pdb=" CA  TYR C 152 "
           pdb=" CB  TYR C 152 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.39  -11.59     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" C   THR C 109 "
           pdb=" N   THR C 109 "
           pdb=" CA  THR C 109 "
           pdb=" CB  THR C 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.58   11.58     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" C   TYR C 152 "
           pdb=" N   TYR C 152 "
           pdb=" CA  TYR C 152 "
           pdb=" CB  TYR C 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.98   11.38     0      2.50e+00 1.60e-01 2.07e+01
  ... (remaining 8526 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1253
       0.082 -    0.164: 806
       0.164 -    0.247: 142
       0.247 -    0.329: 15
       0.329 -    0.411: 2
  Chirality restraints: 2218
  Sorted by residual:
  chirality pdb=" CA  TYR C 152 "
            pdb=" N   TYR C 152 "
            pdb=" C   TYR C 152 "
            pdb=" CB  TYR C 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.22e+00
  chirality pdb=" C3' ANP A1801 "
            pdb=" C2' ANP A1801 "
            pdb=" C4' ANP A1801 "
            pdb=" O3' ANP A1801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.70    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" C3'  DG D  31 "
            pdb=" C4'  DG D  31 "
            pdb=" O3'  DG D  31 "
            pdb=" C2'  DG D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.34   -0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 2215 not shown)

  Planarity restraints: 2319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 168 "   -0.018 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   PHE C 168 "    0.063 2.00e-02 2.50e+03
        pdb=" O   PHE C 168 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ASN C 169 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 623 "    0.034 2.00e-02 2.50e+03   2.38e-02 1.13e+01
        pdb=" CG  TYR A 623 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 623 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 623 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 623 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 623 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 623 "   -0.020 2.00e-02 2.50e+03
        pdb=" OH  TYR A 623 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 215 "   -0.016 2.00e-02 2.50e+03   3.20e-02 1.03e+01
        pdb=" C   LEU A 215 "    0.055 2.00e-02 2.50e+03
        pdb=" O   LEU A 215 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLN A 216 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 2316 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 2457
        2.84 -     3.36: 14179
        3.36 -     3.87: 23177
        3.87 -     4.39: 30108
        4.39 -     4.90: 45552
  Nonbonded interactions: 115473
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 295 "
            pdb=" ND2 ASN B 557 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" O   PHE B 730 "
            pdb=" OG1 THR B 733 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OG  SER C 112 "
            pdb=" O   GLY C 142 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" O   LEU A 295 "
            pdb=" ND2 ASN A 557 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" O   ARG B 232 "
            pdb=" OG  SER B 235 "
     model   vdw
     2.351 3.040
  ... (remaining 115468 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 128 through 659 or resid 672 through 1801))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.090
  Find NCS groups from input model:        0.170
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
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      :  0.014   0.163  14194  Z= 1.038
  Angle     :  1.844  12.159  19480  Z= 1.350
  Chirality :  0.096   0.411   2218
  Planarity :  0.006   0.037   2319
  Dihedral  : 19.505 158.283   5549
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 2.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  6.68 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.20 %
  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: -3.64 (0.17), residues: 1575
  helix: -2.22 (0.15), residues: 704
  sheet: -2.30 (0.36), residues: 156
  loop : -2.55 (0.20), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.034   0.002   ARG A 790 
 TYR   0.044   0.005   TYR A 623 
 PHE   0.032   0.006   PHE A 758 
 TRP   0.022   0.004   TRP A 709 
 HIS   0.010   0.002   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.01388 (14194)
  covalent geometry    : angle       1.84390 (19480)
  hydrogen bonds       : bond        0.25273 (  699)
  hydrogen bonds       : angle       9.38479 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 210
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.8272 (tpt) cc_final: 0.7972 (tpt)
REVERT: A  306 MET cc_start: 0.8625 (ttm) cc_final: 0.8144 (ttt)
REVERT: A  534 LEU cc_start: 0.9130 (mt) cc_final: 0.8490 (mt)
REVERT: A  552 LEU cc_start: 0.9372 (mt) cc_final: 0.9149 (mt)
REVERT: A  633 MET cc_start: 0.7882 (mtp) cc_final: 0.7579 (tpp)
REVERT: A  674 MET cc_start: 0.8519 (mmp) cc_final: 0.8262 (mpp)
REVERT: A  679 ASN cc_start: 0.8367 (t0) cc_final: 0.7778 (m-40)
REVERT: A  750 LEU cc_start: 0.8416 (mt) cc_final: 0.7477 (mm)
REVERT: B  213 LEU cc_start: 0.9597 (mt) cc_final: 0.9268 (mm)
REVERT: B  222 LEU cc_start: 0.8148 (mt) cc_final: 0.7593 (mt)
REVERT: B  260 MET cc_start: 0.8995 (ttt) cc_final: 0.7698 (ttp)
REVERT: B  269 MET cc_start: 0.7955 (ttm) cc_final: 0.7085 (ttm)
REVERT: B  386 ASP cc_start: 0.7718 (t0) cc_final: 0.7508 (m-30)
REVERT: B  609 MET cc_start: 0.8231 (ttm) cc_final: 0.7576 (mtm)
REVERT: B  691 LEU cc_start: 0.8748 (mt) cc_final: 0.8415 (mp)
REVERT: C   28 LYS cc_start: 0.9574 (tttt) cc_final: 0.9255 (ttmm)
REVERT: C   29 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8632 (mt-10)
  outliers start: 15
  outliers final: 1
  residues processed: 222
  average time/residue: 0.1541
  time to fit residues: 45.6697
Evaluate side-chains
  117 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 312 HIS
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.053025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.040395 restraints weight = 119777.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.041707 restraints weight = 77638.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.042581 restraints weight = 56212.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.043272 restraints weight = 44341.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.043730 restraints weight = 36806.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14194  Z= 0.150
  Angle     :  0.626   8.100  19480  Z= 0.336
  Chirality :  0.040   0.192   2218
  Planarity :  0.005   0.088   2319
  Dihedral  : 20.249 153.770   2483
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.73 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.20), residues: 1575
  helix:  0.10 (0.18), residues: 751
  sheet: -1.57 (0.32), residues: 224
  loop : -1.71 (0.24), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 697 
 TYR   0.014   0.002   TYR C 255 
 PHE   0.016   0.002   PHE A 155 
 TRP   0.021   0.002   TRP A 709 
 HIS   0.011   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (14194)
  covalent geometry    : angle       0.62559 (19480)
  hydrogen bonds       : bond        0.04456 (  699)
  hydrogen bonds       : angle       5.27693 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9656 (tpt) cc_final: 0.9259 (tpt)
REVERT: A  302 MET cc_start: 0.9510 (ptm) cc_final: 0.9261 (ptm)
REVERT: A  306 MET cc_start: 0.8994 (ttm) cc_final: 0.8516 (ttt)
REVERT: A  313 MET cc_start: 0.9508 (ttm) cc_final: 0.8887 (mmt)
REVERT: A  348 LEU cc_start: 0.9188 (mt) cc_final: 0.8437 (mt)
REVERT: A  368 MET cc_start: 0.9526 (mmp) cc_final: 0.9137 (mmp)
REVERT: A  574 ASP cc_start: 0.8511 (p0) cc_final: 0.7853 (p0)
REVERT: A  617 MET cc_start: 0.6887 (mpp) cc_final: 0.6658 (ttm)
REVERT: A  633 MET cc_start: 0.8141 (mtp) cc_final: 0.7622 (tpp)
REVERT: A  674 MET cc_start: 0.8045 (mmp) cc_final: 0.7802 (mpp)
REVERT: A  687 TYR cc_start: 0.8998 (m-80) cc_final: 0.8422 (m-80)
REVERT: B  215 LEU cc_start: 0.8841 (pp) cc_final: 0.8141 (pp)
REVERT: B  222 LEU cc_start: 0.8160 (mt) cc_final: 0.7899 (mt)
REVERT: B  260 MET cc_start: 0.8782 (ttt) cc_final: 0.7155 (tmm)
REVERT: B  302 MET cc_start: 0.9599 (ptm) cc_final: 0.9393 (ptm)
REVERT: B  306 MET cc_start: 0.9153 (tpp) cc_final: 0.8894 (tpp)
REVERT: B  313 MET cc_start: 0.9123 (tmm) cc_final: 0.8851 (tmm)
REVERT: B  386 ASP cc_start: 0.8961 (t0) cc_final: 0.8339 (m-30)
REVERT: B  475 ILE cc_start: 0.9179 (mt) cc_final: 0.8916 (tp)
REVERT: B  490 MET cc_start: 0.9466 (mmp) cc_final: 0.9213 (mmm)
REVERT: C   29 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8636 (mt-10)
REVERT: C  133 THR cc_start: 0.9277 (p) cc_final: 0.9066 (p)
REVERT: C  146 GLU cc_start: 0.8279 (pt0) cc_final: 0.7494 (pm20)
REVERT: C  160 PHE cc_start: 0.8886 (m-80) cc_final: 0.8462 (m-80)
REVERT: C  168 PHE cc_start: 0.9171 (t80) cc_final: 0.8934 (t80)
REVERT: C  199 TYR cc_start: 0.8888 (m-80) cc_final: 0.8591 (m-80)
REVERT: C  233 ASP cc_start: 0.8694 (p0) cc_final: 0.7927 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1394
  time to fit residues: 26.4935
Evaluate side-chains
  97 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 120 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 144 optimal weight:    2.9990
   chunk 147 optimal weight:   10.0000
   chunk 118 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 66 optimal weight:    9.9990
   chunk 121 optimal weight:    0.9980
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 543 GLN
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 ASN
B 171 GLN
B 289 ASN
B 544 GLN
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 682 HIS
B 714 ASN
** B 728 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 198 GLN
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.049823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.037320 restraints weight = 122954.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.038545 restraints weight = 79324.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.039411 restraints weight = 57428.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.040030 restraints weight = 45168.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.040481 restraints weight = 37681.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.4723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14194  Z= 0.207
  Angle     :  0.633   7.017  19480  Z= 0.338
  Chirality :  0.040   0.169   2218
  Planarity :  0.005   0.051   2319
  Dihedral  : 19.852 137.640   2483
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.50 %
    Favored  : 97.42 %
  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: -0.62 (0.21), residues: 1575
  helix:  0.70 (0.18), residues: 765
  sheet: -1.47 (0.31), residues: 244
  loop : -1.35 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 656 
 TYR   0.019   0.002   TYR C 124 
 PHE   0.013   0.002   PHE A 467 
 TRP   0.010   0.001   TRP B 202 
 HIS   0.006   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (14194)
  covalent geometry    : angle       0.63283 (19480)
  hydrogen bonds       : bond        0.04599 (  699)
  hydrogen bonds       : angle       5.03450 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9695 (tpt) cc_final: 0.9078 (tpp)
REVERT: A  302 MET cc_start: 0.9444 (ptm) cc_final: 0.9013 (ptm)
REVERT: A  306 MET cc_start: 0.8846 (ttm) cc_final: 0.8462 (ttt)
REVERT: A  313 MET cc_start: 0.9591 (ttm) cc_final: 0.8935 (mmt)
REVERT: A  348 LEU cc_start: 0.9301 (mt) cc_final: 0.8542 (mt)
REVERT: A  368 MET cc_start: 0.9512 (mmp) cc_final: 0.9207 (mmp)
REVERT: A  449 ARG cc_start: 0.9364 (mtm180) cc_final: 0.9070 (ptt-90)
REVERT: A  574 ASP cc_start: 0.8631 (p0) cc_final: 0.7937 (p0)
REVERT: A  609 MET cc_start: 0.8189 (mmm) cc_final: 0.7767 (mmm)
REVERT: A  624 MET cc_start: 0.7990 (mmm) cc_final: 0.7734 (mmm)
REVERT: A  633 MET cc_start: 0.8402 (mtp) cc_final: 0.7956 (tpp)
REVERT: A  674 MET cc_start: 0.8032 (mmp) cc_final: 0.7529 (mpp)
REVERT: A  687 TYR cc_start: 0.9029 (m-80) cc_final: 0.8484 (m-80)
REVERT: A  759 MET cc_start: 0.9156 (mmp) cc_final: 0.8756 (mpp)
REVERT: B  269 MET cc_start: 0.8301 (ttm) cc_final: 0.7758 (ttm)
REVERT: B  302 MET cc_start: 0.9664 (ptm) cc_final: 0.9313 (ptm)
REVERT: B  386 ASP cc_start: 0.9094 (t0) cc_final: 0.8518 (m-30)
REVERT: B  453 ARG cc_start: 0.9734 (tpt90) cc_final: 0.9532 (tpp-160)
REVERT: B  566 ASN cc_start: 0.9034 (m-40) cc_final: 0.8794 (m110)
REVERT: B  609 MET cc_start: 0.8738 (ttm) cc_final: 0.8033 (mtp)
REVERT: C   29 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8446 (mt-10)
REVERT: C  160 PHE cc_start: 0.8649 (m-80) cc_final: 0.8020 (m-80)
REVERT: C  168 PHE cc_start: 0.9218 (t80) cc_final: 0.8957 (t80)
REVERT: C  233 ASP cc_start: 0.8790 (p0) cc_final: 0.7942 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1460
  time to fit residues: 21.0627
Evaluate side-chains
  79 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0270
   chunk 42 optimal weight:    9.9990
   chunk 128 optimal weight:    6.9990
   chunk 140 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 149 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 119 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    3.4046

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

Flipped N/Q/H residues before XYZ refinement:
A 326 GLN
A 339 GLN
A 370 HIS
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 370 HIS
B 483 HIS
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
C 331 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.046970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.034698 restraints weight = 130316.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.035880 restraints weight = 83306.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.036720 restraints weight = 60057.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.037264 restraints weight = 46920.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.037709 restraints weight = 39357.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.6122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14194  Z= 0.265
  Angle     :  0.708  10.435  19480  Z= 0.372
  Chirality :  0.041   0.180   2218
  Planarity :  0.006   0.076   2319
  Dihedral  : 19.900 126.912   2483
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 21.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.11 %
    Favored  : 96.81 %
  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: -0.56 (0.21), residues: 1575
  helix:  0.68 (0.19), residues: 759
  sheet: -1.36 (0.33), residues: 231
  loop : -1.25 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 158 
 TYR   0.022   0.002   TYR A 771 
 PHE   0.021   0.002   PHE B 725 
 TRP   0.014   0.002   TRP B 202 
 HIS   0.012   0.002   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (14194)
  covalent geometry    : angle       0.70797 (19480)
  hydrogen bonds       : bond        0.05027 (  699)
  hydrogen bonds       : angle       5.27840 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9704 (tpt) cc_final: 0.9267 (tpt)
REVERT: A  260 MET cc_start: 0.8621 (tmm) cc_final: 0.8116 (tmm)
REVERT: A  294 VAL cc_start: 0.9176 (t) cc_final: 0.8959 (m)
REVERT: A  302 MET cc_start: 0.9188 (ptm) cc_final: 0.8737 (ptm)
REVERT: A  306 MET cc_start: 0.8636 (ttm) cc_final: 0.8294 (ttt)
REVERT: A  313 MET cc_start: 0.9497 (ttm) cc_final: 0.8995 (mmt)
REVERT: A  348 LEU cc_start: 0.9224 (mt) cc_final: 0.8502 (mt)
REVERT: A  368 MET cc_start: 0.9560 (mmp) cc_final: 0.9353 (mmm)
REVERT: A  574 ASP cc_start: 0.8648 (p0) cc_final: 0.8297 (p0)
REVERT: A  617 MET cc_start: 0.7619 (ttm) cc_final: 0.7253 (tmm)
REVERT: A  633 MET cc_start: 0.8666 (mtp) cc_final: 0.8196 (tpp)
REVERT: A  674 MET cc_start: 0.7932 (mmp) cc_final: 0.7534 (mpp)
REVERT: A  687 TYR cc_start: 0.9241 (m-80) cc_final: 0.8544 (m-80)
REVERT: B  302 MET cc_start: 0.9674 (ptm) cc_final: 0.9317 (ptm)
REVERT: B  386 ASP cc_start: 0.9161 (t0) cc_final: 0.8594 (m-30)
REVERT: B  552 LEU cc_start: 0.9707 (mt) cc_final: 0.9484 (mt)
REVERT: B  574 ASP cc_start: 0.9002 (t0) cc_final: 0.8796 (t0)
REVERT: B  609 MET cc_start: 0.9099 (ttm) cc_final: 0.7904 (mtt)
REVERT: B  673 GLU cc_start: 0.8919 (pt0) cc_final: 0.8574 (pt0)
REVERT: B  758 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7528 (m-10)
REVERT: B  770 SER cc_start: 0.8471 (p) cc_final: 0.8039 (t)
REVERT: C   29 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8458 (mt-10)
REVERT: C  160 PHE cc_start: 0.8928 (m-10) cc_final: 0.8349 (m-80)
REVERT: C  233 ASP cc_start: 0.8775 (p0) cc_final: 0.8175 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1233
  time to fit residues: 17.1766
Evaluate side-chains
  77 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 119 optimal weight:    4.9990
   chunk 33 optimal weight:   10.0000
   chunk 128 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 145 optimal weight:    2.9990
   chunk 159 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   chunk 147 optimal weight:   10.0000
   chunk 151 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.047279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.035150 restraints weight = 129612.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.036333 restraints weight = 82766.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.037166 restraints weight = 59741.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.037764 restraints weight = 46916.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.038179 restraints weight = 39081.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.6410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14194  Z= 0.201
  Angle     :  0.610   7.956  19480  Z= 0.324
  Chirality :  0.039   0.169   2218
  Planarity :  0.004   0.046   2319
  Dihedral  : 19.768 138.151   2483
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  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 are not related in a simple way.
  whole: -0.37 (0.21), residues: 1575
  helix:  0.85 (0.19), residues: 759
  sheet: -1.22 (0.34), residues: 222
  loop : -1.21 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 158 
 TYR   0.020   0.002   TYR A 771 
 PHE   0.015   0.002   PHE B 725 
 TRP   0.015   0.002   TRP B 202 
 HIS   0.008   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (14194)
  covalent geometry    : angle       0.61025 (19480)
  hydrogen bonds       : bond        0.04190 (  699)
  hydrogen bonds       : angle       5.03472 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9679 (tpt) cc_final: 0.9211 (tpt)
REVERT: A  302 MET cc_start: 0.9188 (ptm) cc_final: 0.8441 (ptm)
REVERT: A  306 MET cc_start: 0.8614 (ttm) cc_final: 0.8223 (ttt)
REVERT: A  313 MET cc_start: 0.9490 (ttm) cc_final: 0.9005 (mmt)
REVERT: A  348 LEU cc_start: 0.9444 (mt) cc_final: 0.8723 (mt)
REVERT: A  507 LYS cc_start: 0.9732 (tptp) cc_final: 0.9526 (tppt)
REVERT: A  574 ASP cc_start: 0.8587 (p0) cc_final: 0.8160 (p0)
REVERT: A  609 MET cc_start: 0.9214 (mmm) cc_final: 0.8127 (mmm)
REVERT: A  633 MET cc_start: 0.8649 (mtp) cc_final: 0.8208 (tpp)
REVERT: A  674 MET cc_start: 0.8051 (mmp) cc_final: 0.7838 (mpp)
REVERT: A  687 TYR cc_start: 0.9334 (m-80) cc_final: 0.8527 (m-80)
REVERT: B  269 MET cc_start: 0.8241 (ttm) cc_final: 0.7856 (ttm)
REVERT: B  302 MET cc_start: 0.9702 (ptm) cc_final: 0.9404 (ptm)
REVERT: B  386 ASP cc_start: 0.9110 (t0) cc_final: 0.8742 (m-30)
REVERT: B  552 LEU cc_start: 0.9702 (mt) cc_final: 0.9391 (tp)
REVERT: B  574 ASP cc_start: 0.8974 (t0) cc_final: 0.8760 (t0)
REVERT: B  609 MET cc_start: 0.9039 (ttm) cc_final: 0.8227 (mtp)
REVERT: B  759 MET cc_start: 0.8633 (mpp) cc_final: 0.8230 (mpp)
REVERT: C   28 LYS cc_start: 0.9671 (mtpt) cc_final: 0.9396 (mtpp)
REVERT: C   29 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8372 (mt-10)
REVERT: C  160 PHE cc_start: 0.8935 (m-10) cc_final: 0.8219 (m-80)
REVERT: C  168 PHE cc_start: 0.9555 (t80) cc_final: 0.9270 (t80)
REVERT: C  216 LEU cc_start: 0.9381 (mt) cc_final: 0.9170 (mt)
REVERT: C  233 ASP cc_start: 0.8884 (p0) cc_final: 0.8397 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1168
  time to fit residues: 16.1473
Evaluate side-chains
  72 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 155 optimal weight:    8.9990
   chunk 40 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 157 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.047185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.035021 restraints weight = 129820.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.036201 restraints weight = 83163.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.036999 restraints weight = 60137.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.037590 restraints weight = 47512.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.037993 restraints weight = 39807.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.6811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14194  Z= 0.190
  Angle     :  0.602   7.546  19480  Z= 0.319
  Chirality :  0.039   0.172   2218
  Planarity :  0.005   0.075   2319
  Dihedral  : 19.757 139.267   2483
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  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: -0.24 (0.21), residues: 1575
  helix:  0.92 (0.19), residues: 762
  sheet: -1.22 (0.34), residues: 222
  loop : -1.07 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 198 
 TYR   0.021   0.002   TYR A 771 
 PHE   0.015   0.002   PHE A 155 
 TRP   0.013   0.001   TRP B 202 
 HIS   0.007   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (14194)
  covalent geometry    : angle       0.60179 (19480)
  hydrogen bonds       : bond        0.04075 (  699)
  hydrogen bonds       : angle       5.01571 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9678 (tpt) cc_final: 0.9192 (tpt)
REVERT: A  260 MET cc_start: 0.8962 (tmm) cc_final: 0.8425 (tmm)
REVERT: A  302 MET cc_start: 0.9111 (ptm) cc_final: 0.8856 (ptm)
REVERT: A  306 MET cc_start: 0.8576 (ttm) cc_final: 0.8184 (ttt)
REVERT: A  313 MET cc_start: 0.9456 (ttm) cc_final: 0.9016 (mmt)
REVERT: A  348 LEU cc_start: 0.9272 (mt) cc_final: 0.8515 (mt)
REVERT: A  368 MET cc_start: 0.9555 (mmp) cc_final: 0.9188 (mmp)
REVERT: A  507 LYS cc_start: 0.9728 (tptp) cc_final: 0.9507 (tppt)
REVERT: A  574 ASP cc_start: 0.8581 (p0) cc_final: 0.8218 (p0)
REVERT: A  609 MET cc_start: 0.9151 (mmm) cc_final: 0.8224 (mmm)
REVERT: A  633 MET cc_start: 0.8709 (mtp) cc_final: 0.8194 (tpp)
REVERT: A  687 TYR cc_start: 0.9336 (m-80) cc_final: 0.8528 (m-80)
REVERT: B  269 MET cc_start: 0.7637 (ttm) cc_final: 0.7086 (ttm)
REVERT: B  302 MET cc_start: 0.9681 (ptm) cc_final: 0.9363 (ptm)
REVERT: B  306 MET cc_start: 0.9268 (tpp) cc_final: 0.8604 (tmm)
REVERT: B  386 ASP cc_start: 0.8986 (t0) cc_final: 0.8608 (m-30)
REVERT: B  574 ASP cc_start: 0.8989 (t0) cc_final: 0.8780 (t0)
REVERT: B  609 MET cc_start: 0.9041 (ttm) cc_final: 0.8238 (mtp)
REVERT: B  624 MET cc_start: 0.8951 (mmm) cc_final: 0.8517 (mmt)
REVERT: B  633 MET cc_start: 0.8639 (ppp) cc_final: 0.8314 (ppp)
REVERT: B  673 GLU cc_start: 0.8397 (pt0) cc_final: 0.7944 (pt0)
REVERT: B  674 MET cc_start: 0.8820 (mmt) cc_final: 0.8416 (mmt)
REVERT: B  692 MET cc_start: 0.8513 (mtp) cc_final: 0.8284 (mtp)
REVERT: B  759 MET cc_start: 0.8777 (mpp) cc_final: 0.8272 (mpp)
REVERT: C   28 LYS cc_start: 0.9679 (mtpt) cc_final: 0.9410 (mtpp)
REVERT: C   29 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8312 (pt0)
REVERT: C  160 PHE cc_start: 0.8807 (m-10) cc_final: 0.8236 (m-80)
REVERT: C  233 ASP cc_start: 0.8817 (p0) cc_final: 0.8448 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1236
  time to fit residues: 16.3372
Evaluate side-chains
  71 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 144 optimal weight:    0.9980
   chunk 155 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 158 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.047504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.035567 restraints weight = 125026.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.036831 restraints weight = 78117.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.037709 restraints weight = 55285.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.038319 restraints weight = 42709.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.038752 restraints weight = 35209.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.6947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14194  Z= 0.148
  Angle     :  0.574   7.975  19480  Z= 0.303
  Chirality :  0.039   0.169   2218
  Planarity :  0.004   0.053   2319
  Dihedral  : 19.663 140.237   2483
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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: -0.07 (0.21), residues: 1575
  helix:  1.15 (0.19), residues: 760
  sheet: -1.18 (0.35), residues: 212
  loop : -1.10 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 379 
 TYR   0.014   0.002   TYR A 771 
 PHE   0.015   0.002   PHE C 168 
 TRP   0.012   0.001   TRP B 202 
 HIS   0.005   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14194)
  covalent geometry    : angle       0.57384 (19480)
  hydrogen bonds       : bond        0.03569 (  699)
  hydrogen bonds       : angle       4.82172 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9643 (tpt) cc_final: 0.9169 (tpt)
REVERT: A  260 MET cc_start: 0.8954 (tmm) cc_final: 0.8402 (tmm)
REVERT: A  302 MET cc_start: 0.9087 (ptm) cc_final: 0.8745 (ptm)
REVERT: A  306 MET cc_start: 0.8600 (ttm) cc_final: 0.8190 (ttt)
REVERT: A  313 MET cc_start: 0.9488 (ttm) cc_final: 0.9010 (mmt)
REVERT: A  348 LEU cc_start: 0.9324 (mt) cc_final: 0.8569 (mt)
REVERT: A  368 MET cc_start: 0.9567 (mmp) cc_final: 0.9279 (mmp)
REVERT: A  507 LYS cc_start: 0.9715 (tptp) cc_final: 0.9460 (tppt)
REVERT: A  508 GLU cc_start: 0.9668 (mp0) cc_final: 0.9352 (tp30)
REVERT: A  609 MET cc_start: 0.9303 (mmm) cc_final: 0.7981 (mmm)
REVERT: A  633 MET cc_start: 0.8580 (mtp) cc_final: 0.7919 (tpp)
REVERT: A  687 TYR cc_start: 0.9398 (m-80) cc_final: 0.8548 (m-80)
REVERT: B  187 MET cc_start: 0.8632 (mmt) cc_final: 0.8353 (mmt)
REVERT: B  269 MET cc_start: 0.8543 (ttm) cc_final: 0.7754 (ttm)
REVERT: B  302 MET cc_start: 0.9623 (ptm) cc_final: 0.9326 (ptm)
REVERT: B  306 MET cc_start: 0.9242 (tpp) cc_final: 0.8608 (tmm)
REVERT: B  386 ASP cc_start: 0.9003 (t0) cc_final: 0.8631 (m-30)
REVERT: B  574 ASP cc_start: 0.9011 (t0) cc_final: 0.8781 (t0)
REVERT: B  609 MET cc_start: 0.9013 (ttm) cc_final: 0.7910 (mtt)
REVERT: B  617 MET cc_start: 0.2073 (mmt) cc_final: 0.1817 (mmp)
REVERT: B  624 MET cc_start: 0.8933 (mmm) cc_final: 0.8366 (mmt)
REVERT: B  633 MET cc_start: 0.8536 (ppp) cc_final: 0.8012 (ppp)
REVERT: B  636 ILE cc_start: 0.9582 (pt) cc_final: 0.9173 (mm)
REVERT: B  673 GLU cc_start: 0.8414 (pt0) cc_final: 0.8005 (pt0)
REVERT: B  674 MET cc_start: 0.8620 (mmt) cc_final: 0.8225 (mmt)
REVERT: B  692 MET cc_start: 0.8572 (mtp) cc_final: 0.8280 (mtp)
REVERT: B  759 MET cc_start: 0.8719 (mpp) cc_final: 0.8163 (mpp)
REVERT: C   28 LYS cc_start: 0.9676 (mtpt) cc_final: 0.9428 (mtpp)
REVERT: C  160 PHE cc_start: 0.8865 (m-10) cc_final: 0.8285 (m-80)
REVERT: C  233 ASP cc_start: 0.8852 (p0) cc_final: 0.8352 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1197
  time to fit residues: 15.7859
Evaluate side-chains
  73 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 146 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 143 optimal weight:    0.0470
   chunk 3 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 157 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   chunk 124 optimal weight:    8.9990
   chunk 110 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.0084

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.047262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.035275 restraints weight = 129655.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.036462 restraints weight = 81969.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.037261 restraints weight = 58796.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.037783 restraints weight = 46194.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.038184 restraints weight = 38973.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.7281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14194  Z= 0.169
  Angle     :  0.588  10.394  19480  Z= 0.309
  Chirality :  0.039   0.181   2218
  Planarity :  0.004   0.045   2319
  Dihedral  : 19.732 147.367   2483
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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: -0.04 (0.21), residues: 1575
  helix:  1.15 (0.19), residues: 761
  sheet: -1.20 (0.34), residues: 218
  loop : -1.04 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 200 
 TYR   0.016   0.002   TYR A 771 
 PHE   0.030   0.002   PHE C 168 
 TRP   0.010   0.001   TRP C 239 
 HIS   0.006   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (14194)
  covalent geometry    : angle       0.58780 (19480)
  hydrogen bonds       : bond        0.03784 (  699)
  hydrogen bonds       : angle       4.85330 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9683 (tpt) cc_final: 0.9192 (tpt)
REVERT: A  260 MET cc_start: 0.8874 (tmm) cc_final: 0.8403 (tmm)
REVERT: A  302 MET cc_start: 0.9064 (ptm) cc_final: 0.8723 (ptm)
REVERT: A  306 MET cc_start: 0.8597 (ttm) cc_final: 0.8282 (ttt)
REVERT: A  313 MET cc_start: 0.9447 (ttm) cc_final: 0.9025 (mmt)
REVERT: A  368 MET cc_start: 0.9528 (mmp) cc_final: 0.9245 (mmp)
REVERT: A  507 LYS cc_start: 0.9725 (tptp) cc_final: 0.9522 (tppt)
REVERT: A  508 GLU cc_start: 0.9591 (mp0) cc_final: 0.9358 (tp30)
REVERT: A  609 MET cc_start: 0.9297 (mmm) cc_final: 0.8007 (mmm)
REVERT: A  633 MET cc_start: 0.8597 (mtp) cc_final: 0.7907 (tpp)
REVERT: A  687 TYR cc_start: 0.9415 (m-80) cc_final: 0.8453 (m-80)
REVERT: B  166 MET cc_start: 0.9379 (mmp) cc_final: 0.9134 (mmm)
REVERT: B  187 MET cc_start: 0.8688 (mmt) cc_final: 0.8354 (mmt)
REVERT: B  269 MET cc_start: 0.8013 (ttm) cc_final: 0.7385 (ttm)
REVERT: B  302 MET cc_start: 0.9629 (ptm) cc_final: 0.9357 (ptm)
REVERT: B  306 MET cc_start: 0.9243 (tpp) cc_final: 0.8608 (tmm)
REVERT: B  386 ASP cc_start: 0.8975 (t0) cc_final: 0.8626 (m-30)
REVERT: B  453 ARG cc_start: 0.9504 (tpt90) cc_final: 0.9191 (tpm170)
REVERT: B  574 ASP cc_start: 0.9058 (t0) cc_final: 0.8785 (t0)
REVERT: B  609 MET cc_start: 0.9004 (ttm) cc_final: 0.8214 (mtp)
REVERT: B  633 MET cc_start: 0.8515 (ppp) cc_final: 0.7973 (ppp)
REVERT: B  636 ILE cc_start: 0.9546 (pt) cc_final: 0.9135 (mm)
REVERT: B  673 GLU cc_start: 0.8454 (pt0) cc_final: 0.8067 (pt0)
REVERT: B  674 MET cc_start: 0.8760 (mmt) cc_final: 0.8326 (mmt)
REVERT: B  724 LEU cc_start: 0.9024 (mm) cc_final: 0.8711 (mm)
REVERT: B  739 MET cc_start: 0.8326 (tpp) cc_final: 0.7995 (tpp)
REVERT: B  759 MET cc_start: 0.8668 (mpp) cc_final: 0.8255 (mpp)
REVERT: C   28 LYS cc_start: 0.9563 (mtpt) cc_final: 0.9314 (mtpp)
REVERT: C  160 PHE cc_start: 0.8840 (m-10) cc_final: 0.8125 (m-80)
REVERT: C  189 LEU cc_start: 0.9145 (tp) cc_final: 0.8867 (tp)
REVERT: C  262 MET cc_start: 0.7637 (mmm) cc_final: 0.7425 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1231
  time to fit residues: 15.8480
Evaluate side-chains
  71 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 129 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 118 optimal weight:    0.4980
   chunk 122 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 114 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0020
   chunk 161 optimal weight:   10.0000
   overall best weight:    1.4590

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.047765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.035629 restraints weight = 129148.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.036874 restraints weight = 80654.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.037743 restraints weight = 57327.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.038314 restraints weight = 44464.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.038754 restraints weight = 37198.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.7354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14194  Z= 0.137
  Angle     :  0.565  10.483  19480  Z= 0.297
  Chirality :  0.039   0.213   2218
  Planarity :  0.004   0.047   2319
  Dihedral  : 19.662 145.466   2483
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  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:  0.09 (0.21), residues: 1575
  helix:  1.24 (0.19), residues: 770
  sheet: -1.28 (0.34), residues: 227
  loop : -0.90 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 200 
 TYR   0.015   0.002   TYR C 323 
 PHE   0.018   0.001   PHE C 168 
 TRP   0.012   0.001   TRP B 202 
 HIS   0.004   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (14194)
  covalent geometry    : angle       0.56518 (19480)
  hydrogen bonds       : bond        0.03416 (  699)
  hydrogen bonds       : angle       4.69953 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9647 (tpt) cc_final: 0.9160 (tpt)
REVERT: A  260 MET cc_start: 0.8871 (tmm) cc_final: 0.8417 (tmm)
REVERT: A  302 MET cc_start: 0.9205 (ptm) cc_final: 0.8906 (ptm)
REVERT: A  306 MET cc_start: 0.8611 (ttm) cc_final: 0.8196 (ttt)
REVERT: A  313 MET cc_start: 0.9464 (ttm) cc_final: 0.9009 (mmt)
REVERT: A  348 LEU cc_start: 0.9389 (mt) cc_final: 0.8478 (mt)
REVERT: A  368 MET cc_start: 0.9515 (mmp) cc_final: 0.9154 (mmp)
REVERT: A  508 GLU cc_start: 0.9619 (mp0) cc_final: 0.9371 (tp30)
REVERT: A  609 MET cc_start: 0.9295 (mmm) cc_final: 0.7991 (mmm)
REVERT: A  624 MET cc_start: 0.7539 (mmm) cc_final: 0.6693 (mmt)
REVERT: A  633 MET cc_start: 0.8546 (mtp) cc_final: 0.7879 (tpp)
REVERT: A  687 TYR cc_start: 0.9426 (m-80) cc_final: 0.8438 (m-80)
REVERT: A  692 MET cc_start: 0.6770 (tmm) cc_final: 0.6491 (tmm)
REVERT: B  187 MET cc_start: 0.8707 (mmt) cc_final: 0.8392 (mmt)
REVERT: B  269 MET cc_start: 0.8520 (ttm) cc_final: 0.8265 (ttm)
REVERT: B  302 MET cc_start: 0.9579 (ptm) cc_final: 0.9292 (ptm)
REVERT: B  306 MET cc_start: 0.9309 (tpp) cc_final: 0.8587 (tmm)
REVERT: B  386 ASP cc_start: 0.9054 (t0) cc_final: 0.8686 (m-30)
REVERT: B  453 ARG cc_start: 0.9573 (tpt90) cc_final: 0.9296 (tpm170)
REVERT: B  574 ASP cc_start: 0.9099 (t0) cc_final: 0.8877 (t0)
REVERT: B  593 ASN cc_start: 0.9011 (p0) cc_final: 0.8537 (p0)
REVERT: B  609 MET cc_start: 0.9044 (ttm) cc_final: 0.7907 (mtt)
REVERT: B  617 MET cc_start: 0.1822 (mmt) cc_final: 0.1531 (mmp)
REVERT: B  624 MET cc_start: 0.8940 (mmm) cc_final: 0.8719 (mmt)
REVERT: B  633 MET cc_start: 0.8469 (ppp) cc_final: 0.8147 (ppp)
REVERT: B  673 GLU cc_start: 0.8434 (pt0) cc_final: 0.8043 (pt0)
REVERT: B  674 MET cc_start: 0.8720 (mmt) cc_final: 0.8309 (mmt)
REVERT: B  739 MET cc_start: 0.8590 (tpp) cc_final: 0.8288 (tpp)
REVERT: B  759 MET cc_start: 0.8735 (mpp) cc_final: 0.8221 (mpp)
REVERT: C   28 LYS cc_start: 0.9562 (mtpt) cc_final: 0.9306 (mtpp)
REVERT: C  160 PHE cc_start: 0.8845 (m-10) cc_final: 0.8139 (m-80)
REVERT: C  189 LEU cc_start: 0.9146 (tp) cc_final: 0.8871 (tp)
REVERT: C  262 MET cc_start: 0.7697 (mmm) cc_final: 0.7181 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1197
  time to fit residues: 15.2070
Evaluate side-chains
  69 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 140 optimal weight:    0.0670
   chunk 72 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 138 optimal weight:    7.9990
   chunk 95 optimal weight:    0.2980
   chunk 120 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 88 optimal weight:    9.9990
   chunk 145 optimal weight:    2.9990
   overall best weight:    1.0322

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.048437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.036230 restraints weight = 129073.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.037483 restraints weight = 80929.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.038354 restraints weight = 57681.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.038955 restraints weight = 44953.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.039391 restraints weight = 37427.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.7405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14194  Z= 0.120
  Angle     :  0.547   7.933  19480  Z= 0.288
  Chirality :  0.039   0.199   2218
  Planarity :  0.004   0.046   2319
  Dihedral  : 19.629 146.928   2483
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  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:  0.16 (0.21), residues: 1575
  helix:  1.34 (0.19), residues: 769
  sheet: -1.32 (0.33), residues: 239
  loop : -0.86 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 200 
 TYR   0.012   0.001   TYR A 623 
 PHE   0.015   0.001   PHE C 168 
 TRP   0.010   0.001   TRP B 202 
 HIS   0.004   0.001   HIS A 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14194)
  covalent geometry    : angle       0.54733 (19480)
  hydrogen bonds       : bond        0.03196 (  699)
  hydrogen bonds       : angle       4.63847 ( 1928)

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

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

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3150 Ramachandran restraints generated.
    1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 MET cc_start: 0.9644 (tpt) cc_final: 0.9190 (tpt)
REVERT: A  260 MET cc_start: 0.8827 (tmm) cc_final: 0.8386 (tmm)
REVERT: A  302 MET cc_start: 0.9228 (ptm) cc_final: 0.8937 (ptm)
REVERT: A  306 MET cc_start: 0.8624 (ttm) cc_final: 0.8195 (ttt)
REVERT: A  313 MET cc_start: 0.9457 (ttm) cc_final: 0.9008 (mmt)
REVERT: A  348 LEU cc_start: 0.9392 (mt) cc_final: 0.8485 (mt)
REVERT: A  368 MET cc_start: 0.9521 (mmp) cc_final: 0.9140 (mmp)
REVERT: A  508 GLU cc_start: 0.9621 (mp0) cc_final: 0.9368 (tp30)
REVERT: A  609 MET cc_start: 0.9272 (mmm) cc_final: 0.7873 (mmm)
REVERT: A  624 MET cc_start: 0.7511 (mmm) cc_final: 0.6877 (mmt)
REVERT: A  633 MET cc_start: 0.8504 (mtp) cc_final: 0.7872 (tpp)
REVERT: B  166 MET cc_start: 0.9457 (mmp) cc_final: 0.9156 (mmm)
REVERT: B  187 MET cc_start: 0.8628 (mmt) cc_final: 0.8024 (mmm)
REVERT: B  269 MET cc_start: 0.8465 (ttm) cc_final: 0.8063 (ttm)
REVERT: B  302 MET cc_start: 0.9556 (ptm) cc_final: 0.9284 (ptm)
REVERT: B  306 MET cc_start: 0.9349 (tpp) cc_final: 0.8706 (tmm)
REVERT: B  386 ASP cc_start: 0.9125 (t0) cc_final: 0.8731 (m-30)
REVERT: B  574 ASP cc_start: 0.9102 (t0) cc_final: 0.8876 (t0)
REVERT: B  593 ASN cc_start: 0.9112 (p0) cc_final: 0.8718 (p0)
REVERT: B  609 MET cc_start: 0.9062 (ttm) cc_final: 0.7868 (mtt)
REVERT: B  617 MET cc_start: 0.2062 (mmt) cc_final: 0.1676 (mmp)
REVERT: B  633 MET cc_start: 0.8522 (ppp) cc_final: 0.8192 (ppp)
REVERT: B  692 MET cc_start: 0.8519 (mtm) cc_final: 0.7553 (mmm)
REVERT: B  739 MET cc_start: 0.8680 (tpp) cc_final: 0.8288 (tpp)
REVERT: B  759 MET cc_start: 0.8955 (mpp) cc_final: 0.8604 (mpp)
REVERT: C   28 LYS cc_start: 0.9544 (mtpt) cc_final: 0.9328 (mtpp)
REVERT: C  160 PHE cc_start: 0.8855 (m-10) cc_final: 0.8150 (m-80)
REVERT: C  189 LEU cc_start: 0.9106 (tp) cc_final: 0.8801 (tp)
REVERT: C  262 MET cc_start: 0.8003 (mmm) cc_final: 0.6865 (mmm)
REVERT: C  263 MET cc_start: 0.6332 (tpp) cc_final: 0.5818 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1247
  time to fit residues: 15.4731
Evaluate side-chains
  65 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 164
   random chunks:
   chunk 146 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9980
   chunk 144 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0980
   chunk 126 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0980
   chunk 109 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 GLN
** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.047422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.035304 restraints weight = 130015.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.036544 restraints weight = 81855.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.037382 restraints weight = 58373.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.037971 restraints weight = 45413.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.038367 restraints weight = 37882.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.7623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14194  Z= 0.158
  Angle     :  0.578  10.741  19480  Z= 0.303
  Chirality :  0.039   0.193   2218
  Planarity :  0.004   0.046   2319
  Dihedral  : 19.703 150.646   2483
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  0.13 (0.21), residues: 1575
  helix:  1.26 (0.19), residues: 771
  sheet: -1.26 (0.34), residues: 226
  loop : -0.86 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 200 
 TYR   0.013   0.002   TYR A 771 
 PHE   0.015   0.002   PHE C 168 
 TRP   0.009   0.001   TRP C 239 
 HIS   0.007   0.001   HIS A 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (14194)
  covalent geometry    : angle       0.57827 (19480)
  hydrogen bonds       : bond        0.03622 (  699)
  hydrogen bonds       : angle       4.74369 ( 1928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1917.36 seconds
wall clock time: 34 minutes 9.71 seconds (2049.71 seconds total)