Starting phenix.real_space_refine
on Wed Jul 24 03:05:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/07_2024/8tz8_41737_trim.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.064
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      87      5.16       5
     C    8179      2.51       5
     N    1927      2.21       5
     O    2130      1.98       5
     H   12101      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B PHE  131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B TYR  357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "B PHE  526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "C PHE  488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 24426
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8129
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 69
    Chain: "B"
      Number of atoms: 8076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8076
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 77
    Chain: "C"
      Number of atoms: 8076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8076
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 77
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 66
          Unusual residues: {'LBN': 1, 'XMO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 9
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'XMO': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'LBN': 1, 'XMO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 19
  Time building chain proxies: 11.08, per 1000 atoms: 0.45
  Number of scatterers: 24426
  At special positions: 0
  Unit cell: (131.76, 129.6, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      87     16.00
     P       2     15.00
     O    2130      8.00
     N    1927      7.00
     C    8179      6.00
     H   12101      1.00
    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  - 3.50
        Amino acid           : False - 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: 19.81
  Conformation dependent library (CDL) restraints added in 2.9 seconds
  

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2946

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 1 sheets defined
      88.0% alpha, 0.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 103 through 130
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 157 through 203
      Proline residue:  A 167  - end of helix
      removed outlier: 4.813A  pdb=" N   PHE A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   TRP A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   TRP A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 223
      removed outlier: 3.968A  pdb=" N   LEU A 207 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 251
      removed outlier: 4.551A  pdb=" N   VAL A 235 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 270
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 4.245A  pdb=" N   GLY A 276 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 287
    Processing helix  chain 'A' and resid 288 through 312
      removed outlier: 4.425A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 330
      removed outlier: 3.690A  pdb=" N   VAL A 324 " --> pdb=" O   LYS A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.638A  pdb=" N   ARG A 355 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
    Processing helix  chain 'A' and resid 362 through 375
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 381 through 388
      removed outlier: 3.544A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 414
      removed outlier: 4.222A  pdb=" N   ALA A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 423 through 429
    Processing helix  chain 'A' and resid 437 through 479
      removed outlier: 3.816A  pdb=" N   SER A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   LEU A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 487 through 496
    Processing helix  chain 'A' and resid 496 through 503
    Processing helix  chain 'A' and resid 506 through 523
      removed outlier: 4.272A  pdb=" N   PHE A 511 " --> pdb=" O   TRP A 507 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   MET A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 542
      removed outlier: 4.108A  pdb=" N   ALA A 528 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 566
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 4.350A  pdb=" N   GLY A 576 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE A 577 " --> pdb=" O   GLY A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 619
      removed outlier: 3.793A  pdb=" N   ALA A 595 " --> pdb=" O   ARG A 591 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   MET A 598 " --> pdb=" O   THR A 594 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   ARG A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 618 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 103
    Processing helix  chain 'B' and resid 103 through 130
    Processing helix  chain 'B' and resid 134 through 157
    Processing helix  chain 'B' and resid 157 through 203
      Proline residue:  B 167  - end of helix
      removed outlier: 4.655A  pdb=" N   PHE B 177 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 5.959A  pdb=" N   TRP B 178 " --> pdb=" O   SER B 174 " (cutoff:3.500A)
      removed outlier: 5.213A  pdb=" N   TRP B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 223
      removed outlier: 3.681A  pdb=" N   LEU B 207 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 4.550A  pdb=" N   VAL B 235 " --> pdb=" O   TYR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 271
    Processing helix  chain 'B' and resid 272 through 282
      removed outlier: 4.198A  pdb=" N   GLY B 276 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 312
      removed outlier: 4.588A  pdb=" N   LEU B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      Proline residue:  B 296  - end of helix
    Processing helix  chain 'B' and resid 312 through 329
      removed outlier: 3.630A  pdb=" N   TRP B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   VAL B 324 " --> pdb=" O   LYS B 320 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 342
    Processing helix  chain 'B' and resid 349 through 361
      Proline residue:  B 356  - end of helix
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 362 through 376
      removed outlier: 3.764A  pdb=" N   THR B 376 " --> pdb=" O   ALA B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 378 through 388
      removed outlier: 3.736A  pdb=" N   LEU B 382 " --> pdb=" O   ALA B 378 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY B 383 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA B 384 " --> pdb=" O   SER B 380 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER B 387 " --> pdb=" O   GLY B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 414
      removed outlier: 4.195A  pdb=" N   ALA B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      Proline residue:  B 404  - end of helix
    Processing helix  chain 'B' and resid 423 through 429
    Processing helix  chain 'B' and resid 437 through 448
    Processing helix  chain 'B' and resid 449 through 479
    Processing helix  chain 'B' and resid 487 through 496
      removed outlier: 3.621A  pdb=" N   TYR B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 504
      removed outlier: 3.597A  pdb=" N   ALA B 500 " --> pdb=" O   PHE B 496 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLY B 504 " --> pdb=" O   ALA B 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 523
      removed outlier: 4.125A  pdb=" N   PHE B 511 " --> pdb=" O   TRP B 507 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   MET B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU B 516 " --> pdb=" O   MET B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 542
      removed outlier: 3.931A  pdb=" N   ALA B 528 " --> pdb=" O   ASN B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 566
    Processing helix  chain 'B' and resid 574 through 586
      removed outlier: 3.613A  pdb=" N   VAL B 578 " --> pdb=" O   SER B 574 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   SER B 584 " --> pdb=" O   GLY B 580 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET B 585 " --> pdb=" O   GLY B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 596
      removed outlier: 3.616A  pdb=" N   THR B 594 " --> pdb=" O   LYS B 590 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA B 595 " --> pdb=" O   ARG B 591 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY B 596 " --> pdb=" O   ASP B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 619
    Processing helix  chain 'C' and resid 91 through 103
    Processing helix  chain 'C' and resid 103 through 130
    Processing helix  chain 'C' and resid 130 through 157
      Proline residue:  C 136  - end of helix
    Processing helix  chain 'C' and resid 157 through 198
      Proline residue:  C 167  - end of helix
      removed outlier: 4.430A  pdb=" N   PHE C 177 " --> pdb=" O   ASP C 173 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   TRP C 178 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   TRP C 181 " --> pdb=" O   PHE C 177 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL C 182 " --> pdb=" O   TRP C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 203
    Processing helix  chain 'C' and resid 203 through 223
      removed outlier: 3.871A  pdb=" N   LEU C 207 " --> pdb=" O   GLY C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 252
      removed outlier: 3.709A  pdb=" N   GLY C 238 " --> pdb=" O   PRO C 234 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR C 252 " --> pdb=" O   LEU C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 271
    Processing helix  chain 'C' and resid 271 through 281
      removed outlier: 4.020A  pdb=" N   ALA C 275 " --> pdb=" O   GLY C 271 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   PHE C 279 " --> pdb=" O   ALA C 275 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL C 280 " --> pdb=" O   GLY C 276 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 287
    Processing helix  chain 'C' and resid 288 through 312
      removed outlier: 4.220A  pdb=" N   LEU C 295 " --> pdb=" O   ALA C 291 " (cutoff:3.500A)
      Proline residue:  C 296  - end of helix
    Processing helix  chain 'C' and resid 312 through 330
      removed outlier: 3.855A  pdb=" N   VAL C 324 " --> pdb=" O   LYS C 320 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   MET C 325 " --> pdb=" O   VAL C 321 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 342
    Processing helix  chain 'C' and resid 349 through 361
      removed outlier: 3.573A  pdb=" N   ARG C 355 " --> pdb=" O   LEU C 352 " (cutoff:3.500A)
      Proline residue:  C 356  - end of helix
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 362 through 375
      removed outlier: 3.828A  pdb=" N   GLY C 373 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 388
      removed outlier: 3.965A  pdb=" N   GLY C 383 " --> pdb=" O   GLY C 379 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   ALA C 384 " --> pdb=" O   SER C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 414
      Proline residue:  C 404  - end of helix
      removed outlier: 3.850A  pdb=" N   LEU C 407 " --> pdb=" O   ALA C 403 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 423 through 429
    Processing helix  chain 'C' and resid 437 through 449
      removed outlier: 3.908A  pdb=" N   SER C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 449 through 480
      removed outlier: 3.816A  pdb=" N   MET C 480 " --> pdb=" O   TRP C 476 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 487 through 496
      removed outlier: 3.573A  pdb=" N   TYR C 494 " --> pdb=" O   VAL C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 503
    Processing helix  chain 'C' and resid 506 through 523
      removed outlier: 4.173A  pdb=" N   PHE C 511 " --> pdb=" O   TRP C 507 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   MET C 512 " --> pdb=" O   GLN C 508 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 542
      removed outlier: 3.908A  pdb=" N   ALA C 528 " --> pdb=" O   ASN C 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 566
    Processing helix  chain 'C' and resid 573 through 586
      removed outlier: 4.558A  pdb=" N   ILE C 577 " --> pdb=" O   GLY C 573 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 589 through 618
      removed outlier: 3.600A  pdb=" N   THR C 594 " --> pdb=" O   LYS C 590 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA C 595 " --> pdb=" O   ARG C 591 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   MET C 598 " --> pdb=" O   THR C 594 " (cutoff:3.500A)
      removed outlier: 5.352A  pdb=" N   ARG C 599 " --> pdb=" O   ALA C 595 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA C 600 " --> pdb=" O   GLY C 596 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547

    964 hydrogen bonds defined for protein.
    2850 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 8.61

  Time building geometry restraints manager: 20.82 seconds

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

  Histogram of bond lengths:
        0.81 -     1.01: 12083
        1.01 -     1.21: 28
        1.21 -     1.41: 5215
        1.41 -     1.61: 7272
        1.61 -     1.81: 163
  Bond restraints: 24761
  Sorted by residual:
  bond pdb=" C11 XMO A 801 "
       pdb=" O12 XMO A 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.681 -0.283 2.00e-02 2.50e+03 2.01e+02
  bond pdb=" C11 XMO C 801 "
       pdb=" O12 XMO C 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.677 -0.279 2.00e-02 2.50e+03 1.94e+02
  bond pdb=" C11 XMO B 801 "
       pdb=" O12 XMO B 801 "
    ideal  model  delta    sigma   weight residual
    1.398  1.676 -0.278 2.00e-02 2.50e+03 1.93e+02
  bond pdb=" C10 XMO C 801 "
       pdb=" C11 XMO C 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.289  0.245 2.00e-02 2.50e+03 1.50e+02
  bond pdb=" C10 XMO B 801 "
       pdb=" C11 XMO B 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.289  0.245 2.00e-02 2.50e+03 1.49e+02
  ... (remaining 24756 not shown)

  Histogram of bond angle deviations from ideal:
       99.72 -   106.58: 385
      106.58 -   113.44: 28495
      113.44 -   120.29: 8696
      120.29 -   127.15: 6868
      127.15 -   134.01: 171
  Bond angle restraints: 44615
  Sorted by residual:
  angle pdb=" O1  LBN C 802 "
        pdb=" P1  LBN C 802 "
        pdb=" O2  LBN C 802 "
      ideal   model   delta    sigma   weight residual
      93.45  109.56  -16.11 3.00e+00 1.11e-01 2.88e+01
  angle pdb=" O1  LBN A 802 "
        pdb=" P1  LBN A 802 "
        pdb=" O2  LBN A 802 "
      ideal   model   delta    sigma   weight residual
      93.45  109.49  -16.04 3.00e+00 1.11e-01 2.86e+01
  angle pdb=" O3  LBN C 802 "
        pdb=" P1  LBN C 802 "
        pdb=" O4  LBN C 802 "
      ideal   model   delta    sigma   weight residual
     119.36  109.56    9.80 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" O3  LBN A 802 "
        pdb=" P1  LBN A 802 "
        pdb=" O4  LBN A 802 "
      ideal   model   delta    sigma   weight residual
     119.36  109.64    9.72 3.00e+00 1.11e-01 1.05e+01
  angle pdb=" C02 XMO B 801 "
        pdb=" C04 XMO B 801 "
        pdb=" O06 XMO B 801 "
      ideal   model   delta    sigma   weight residual
     111.45  120.15   -8.70 3.00e+00 1.11e-01 8.40e+00
  ... (remaining 44610 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.98: 11444
       32.98 -    65.96: 362
       65.96 -    98.94: 15
       98.94 -   131.92: 4
      131.92 -   164.89: 4
  Dihedral angle restraints: 11829
    sinusoidal: 6099
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" C01 XMO C 801 "
           pdb=" C02 XMO C 801 "
           pdb=" C04 XMO C 801 "
           pdb=" O06 XMO C 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     296.92  132.03  164.89     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" C01 XMO C 801 "
           pdb=" C02 XMO C 801 "
           pdb=" C04 XMO C 801 "
           pdb=" O05 XMO C 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     116.78  -47.37  164.15     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" C01 XMO B 801 "
           pdb=" C02 XMO B 801 "
           pdb=" C04 XMO B 801 "
           pdb=" O06 XMO B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     296.92  148.56  148.36     1      3.00e+01 1.11e-03 1.97e+01
  ... (remaining 11826 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1873
       0.074 -    0.148: 114
       0.148 -    0.222: 1
       0.222 -    0.296: 0
       0.296 -    0.369: 3
  Chirality restraints: 1991
  Sorted by residual:
  chirality pdb=" C10 XMO B 801 "
            pdb=" C09 XMO B 801 "
            pdb=" C11 XMO B 801 "
            pdb=" O22 XMO B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.37    0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" C10 XMO C 801 "
            pdb=" C09 XMO C 801 "
            pdb=" C11 XMO C 801 "
            pdb=" O22 XMO C 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.38    0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" C10 XMO A 801 "
            pdb=" C09 XMO A 801 "
            pdb=" C11 XMO A 801 "
            pdb=" O22 XMO A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.74    2.42    0.32 2.00e-01 2.50e+01 2.61e+00
  ... (remaining 1988 not shown)

  Planarity restraints: 3631
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 290 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   PHE C 290 "    0.033 2.00e-02 2.50e+03
        pdb=" O   PHE C 290 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA C 291 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 599 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.52e+00
        pdb=" C   ARG A 599 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ARG A 599 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA A 600 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 608 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.16e+00
        pdb=" C   CYS A 608 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   CYS A 608 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 609 "    0.010 2.00e-02 2.50e+03
  ... (remaining 3628 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 901
        2.18 -     2.79: 46951
        2.79 -     3.39: 67449
        3.39 -     4.00: 83999
        4.00 -     4.60: 133737
  Nonbonded interactions: 333037
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 206 "
            pdb=" H   GLN A 206 "
     model   vdw
     1.580 1.850
  nonbonded pdb=" O   SER A 451 "
            pdb="HD22 ASN A 455 "
     model   vdw
     1.588 1.850
  nonbonded pdb=" H   ARG A 436 "
            pdb=" OE1 GLU A 440 "
     model   vdw
     1.593 1.850
  nonbonded pdb=" OE1 GLU A 525 "
            pdb=" H   GLU A 525 "
     model   vdw
     1.597 1.850
  nonbonded pdb=" O   LEU C 248 "
            pdb=" HG1 THR C 252 "
     model   vdw
     1.608 1.850
  ... (remaining 333032 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 90 through 104 or (resid 105 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 106 or (resid 107 thro \ 
ugh 110 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 111 through 113 or (resid 114 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 115 through 176 or (resid 17 \ 
7 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 178 through 420 or (resid 421 and (name N or name CA or name C or name  \ 
O or name CB or name H or name HA )) or resid 422 through 435 or (resid 436 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 437 through 622 or resid 801))
  selection = (chain 'B' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ 
sid 434 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ 
))
  selection = (chain 'C' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ 
sid 434 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ 
))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:             0.340
  Extract box with map and model:          0.740
  Check model and map are aligned:         0.150
  Set scattering table:                    0.190
  Process input model:                     76.850
  Find NCS groups from input model:        1.070
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   83.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
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      :  0.010   0.283  12660  Z= 0.614
  Angle     :  0.622  16.106  17229  Z= 0.301
  Chirality :  0.039   0.369   1991
  Planarity :  0.004   0.039   2089
  Dihedral  : 13.771 164.894   4351
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.21), residues: 1593
  helix:  2.31 (0.14), residues: 1296
  sheet:  None (None), residues: 0
  loop : -0.55 (0.31), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 288 
 PHE   0.018   0.001   PHE C 413 
 TYR   0.009   0.001   TYR A 357 
 ARG   0.002   0.000   ARG B 319 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  302 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 302
  time to evaluate  : 1.894 
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  181 TRP cc_start: 0.6533 (m100) cc_final: 0.6121 (m100)
REVERT: A  264 LYS cc_start: 0.7884 (mttt) cc_final: 0.7602 (mtpt)
REVERT: A  345 ILE cc_start: 0.8286 (mm) cc_final: 0.8057 (mp)
REVERT: A  350 SER cc_start: 0.8346 (t) cc_final: 0.8088 (t)
REVERT: A  497 MET cc_start: 0.7602 (tmm) cc_final: 0.7320 (tmm)
REVERT: B  370 MET cc_start: 0.7987 (mtm) cc_final: 0.7731 (mtp)
REVERT: B  458 VAL cc_start: 0.8301 (t) cc_final: 0.8020 (t)
REVERT: B  585 MET cc_start: 0.8711 (mtt) cc_final: 0.8457 (mtt)
REVERT: C  242 GLN cc_start: 0.8341 (mt0) cc_final: 0.8117 (mt0)
REVERT: C  357 TYR cc_start: 0.8340 (m-80) cc_final: 0.8100 (m-80)
REVERT: C  370 MET cc_start: 0.8805 (mtm) cc_final: 0.8569 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 302
  average time/residue: 0.4788
  time to fit residues: 212.1565
Evaluate side-chains
  220 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    0.9990
   chunk 120 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    0.1980
   chunk 64 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 144 optimal weight:    2.9990
   overall best weight:    0.8388

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  12660  Z= 0.161
  Angle     :  0.465   5.292  17229  Z= 0.245
  Chirality :  0.035   0.132   1991
  Planarity :  0.003   0.046   2089
  Dihedral  : 10.222 163.582   1827
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  7.82 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.33 (0.21), residues: 1593
  helix:  2.70 (0.14), residues: 1315
  sheet:  None (None), residues: 0
  loop : -0.36 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 132 
 PHE   0.016   0.001   PHE C 413 
 TYR   0.010   0.001   TYR A 357 
 ARG   0.003   0.000   ARG C 251 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  241 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 222
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 TRP cc_start: 0.6594 (m100) cc_final: 0.6082 (m100)
REVERT: A  264 LYS cc_start: 0.7940 (mttt) cc_final: 0.7681 (mtpt)
REVERT: A  428 MET cc_start: 0.8081 (mmt) cc_final: 0.7773 (mmt)
REVERT: A  497 MET cc_start: 0.7510 (tmm) cc_final: 0.7225 (tmm)
REVERT: B  158 GLU cc_start: 0.7257 (pm20) cc_final: 0.7044 (pm20)
REVERT: B  242 GLN cc_start: 0.8278 (mt0) cc_final: 0.7938 (mt0)
REVERT: B  370 MET cc_start: 0.7839 (mtm) cc_final: 0.7521 (mtp)
REVERT: B  458 VAL cc_start: 0.8313 (t) cc_final: 0.8016 (t)
REVERT: B  503 MET cc_start: 0.9019 (mtp) cc_final: 0.8670 (mtp)
REVERT: B  598 MET cc_start: 0.7420 (tpt) cc_final: 0.7063 (tpt)
REVERT: C  219 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7736 (mp)
REVERT: C  357 TYR cc_start: 0.8348 (m-80) cc_final: 0.8107 (m-80)
REVERT: C  370 MET cc_start: 0.8571 (mtm) cc_final: 0.8367 (mtm)
  outliers start: 19
  outliers final: 12
  residues processed: 230
  average time/residue: 0.4475
  time to fit residues: 155.9845
Evaluate side-chains
  221 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 208
  time to evaluate  : 1.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  620 ASN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  214 ILE
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  458 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 120 optimal weight:    0.4980
   chunk 98 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 144 optimal weight:    2.9990
   chunk 156 optimal weight:    3.9990
   chunk 128 optimal weight:    1.9990
   chunk 143 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12660  Z= 0.205
  Angle     :  0.462   5.072  17229  Z= 0.245
  Chirality :  0.035   0.145   1991
  Planarity :  0.003   0.044   2089
  Dihedral  :  8.586 119.914   1827
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.98 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.30 (0.21), residues: 1593
  helix:  2.69 (0.14), residues: 1320
  sheet:  None (None), residues: 0
  loop : -0.50 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.019   0.001   PHE C 413 
 TYR   0.012   0.001   TYR B 231 
 ARG   0.002   0.000   ARG A 436 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  228 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 207
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 TRP cc_start: 0.6657 (m100) cc_final: 0.6100 (m100)
REVERT: A  264 LYS cc_start: 0.7932 (mttt) cc_final: 0.7682 (mtpt)
REVERT: A  348 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8273 (p)
REVERT: A  428 MET cc_start: 0.8096 (mmt) cc_final: 0.7718 (mmt)
REVERT: A  480 MET cc_start: 0.8188 (mmt) cc_final: 0.7746 (mmt)
REVERT: A  497 MET cc_start: 0.7651 (tmm) cc_final: 0.7401 (tmm)
REVERT: B  370 MET cc_start: 0.7927 (mtm) cc_final: 0.7628 (mtp)
REVERT: B  444 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6724 (tt0)
REVERT: B  598 MET cc_start: 0.7534 (tpt) cc_final: 0.7117 (tpt)
REVERT: C  219 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7838 (mp)
REVERT: C  257 MET cc_start: 0.6857 (ptt) cc_final: 0.6480 (ptp)
REVERT: C  357 TYR cc_start: 0.8344 (m-80) cc_final: 0.8127 (m-80)
REVERT: C  370 MET cc_start: 0.8507 (mtm) cc_final: 0.8301 (mtm)
  outliers start: 21
  outliers final: 14
  residues processed: 220
  average time/residue: 0.4357
  time to fit residues: 148.3741
Evaluate side-chains
  209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 193
  time to evaluate  : 1.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain A residue  620 ASN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 142 optimal weight:    1.9990
   chunk 108 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 145 optimal weight:    2.9990
   chunk 153 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12660  Z= 0.254
  Angle     :  0.481   5.080  17229  Z= 0.258
  Chirality :  0.036   0.149   1991
  Planarity :  0.004   0.045   2089
  Dihedral  :  8.125  98.608   1827
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.50 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.09 (0.21), residues: 1593
  helix:  2.55 (0.14), residues: 1320
  sheet:  None (None), residues: 0
  loop : -0.62 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 150 
 HIS   0.004   0.001   HIS A 288 
 PHE   0.020   0.001   PHE C 413 
 TYR   0.012   0.001   TYR A 357 
 ARG   0.002   0.000   ARG A 436 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  211 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 193
  time to evaluate  : 1.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7965 (mttt) cc_final: 0.7683 (mtpt)
REVERT: B  158 GLU cc_start: 0.6913 (pm20) cc_final: 0.6500 (pm20)
REVERT: B  370 MET cc_start: 0.7978 (mtm) cc_final: 0.7711 (mtp)
REVERT: B  444 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6730 (tt0)
REVERT: B  503 MET cc_start: 0.9037 (mtp) cc_final: 0.8650 (mtp)
REVERT: B  598 MET cc_start: 0.7639 (tpt) cc_final: 0.7160 (tpt)
REVERT: C  219 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7899 (mp)
REVERT: C  257 MET cc_start: 0.6920 (ptt) cc_final: 0.6539 (ptp)
  outliers start: 18
  outliers final: 15
  residues processed: 207
  average time/residue: 0.4313
  time to fit residues: 137.5384
Evaluate side-chains
  201 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 185
  time to evaluate  : 1.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Chi-restraints excluded: chain C residue  506 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 114 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 131 optimal weight:    1.9990
   chunk 106 optimal weight:   30.0000
   chunk 0 optimal weight:   40.0000
   chunk 78 optimal weight:    1.9990
   chunk 137 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
C 169 GLN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12660  Z= 0.258
  Angle     :  0.477   5.101  17229  Z= 0.256
  Chirality :  0.036   0.142   1991
  Planarity :  0.004   0.049   2089
  Dihedral  :  7.940  94.993   1827
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 10.61 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.21), residues: 1593
  helix:  2.49 (0.14), residues: 1310
  sheet:  None (None), residues: 0
  loop : -0.52 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 178 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.018   0.001   PHE B 413 
 TYR   0.012   0.001   TYR A 357 
 ARG   0.003   0.000   ARG A 436 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 1.805 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8038 (mttt) cc_final: 0.7750 (mtpt)
REVERT: A  428 MET cc_start: 0.8180 (mmt) cc_final: 0.7711 (mmp)
REVERT: A  430 MET cc_start: 0.8136 (mtt) cc_final: 0.7836 (mtt)
REVERT: B  370 MET cc_start: 0.8032 (mtm) cc_final: 0.7612 (mtp)
REVERT: B  503 MET cc_start: 0.9011 (mtp) cc_final: 0.8610 (mtp)
REVERT: B  598 MET cc_start: 0.7656 (tpt) cc_final: 0.7173 (tpt)
REVERT: C  219 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7927 (mp)
REVERT: C  257 MET cc_start: 0.6861 (ptt) cc_final: 0.6493 (ptp)
  outliers start: 21
  outliers final: 15
  residues processed: 209
  average time/residue: 0.4309
  time to fit residues: 139.4953
Evaluate side-chains
  205 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 189
  time to evaluate  : 1.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Chi-restraints excluded: chain C residue  506 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 153 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 148 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12660  Z= 0.288
  Angle     :  0.492   5.645  17229  Z= 0.265
  Chirality :  0.036   0.151   1991
  Planarity :  0.004   0.050   2089
  Dihedral  :  7.836  91.666   1827
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.41 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.21), residues: 1593
  helix:  2.39 (0.14), residues: 1310
  sheet:  None (None), residues: 0
  loop : -0.64 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 178 
 HIS   0.004   0.001   HIS A 288 
 PHE   0.018   0.001   PHE C 413 
 TYR   0.013   0.001   TYR A 357 
 ARG   0.002   0.000   ARG A 436 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  219 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 1.619 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8061 (mttt) cc_final: 0.7775 (mtpt)
REVERT: A  350 SER cc_start: 0.8218 (t) cc_final: 0.7593 (p)
REVERT: A  428 MET cc_start: 0.8182 (mmt) cc_final: 0.7760 (mmp)
REVERT: A  430 MET cc_start: 0.8201 (mtt) cc_final: 0.7908 (mtt)
REVERT: B  112 TRP cc_start: 0.6239 (t60) cc_final: 0.5736 (t-100)
REVERT: B  370 MET cc_start: 0.8065 (mtm) cc_final: 0.7636 (mtp)
REVERT: B  503 MET cc_start: 0.9016 (mtp) cc_final: 0.8614 (mtp)
REVERT: B  598 MET cc_start: 0.7679 (tpt) cc_final: 0.7200 (tpt)
REVERT: C  219 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7975 (mp)
REVERT: C  257 MET cc_start: 0.6981 (ptt) cc_final: 0.6615 (ptp)
REVERT: C  413 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8457 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 214
  average time/residue: 0.4368
  time to fit residues: 147.3141
Evaluate side-chains
  211 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 192
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  257 MET
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain B residue  133 ARG
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Chi-restraints excluded: chain C residue  506 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 153 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 61 optimal weight:   10.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12660  Z= 0.226
  Angle     :  0.463   5.120  17229  Z= 0.247
  Chirality :  0.035   0.139   1991
  Planarity :  0.004   0.050   2089
  Dihedral  :  7.539  84.752   1827
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 12.37 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.98 (0.21), residues: 1593
  helix:  2.49 (0.15), residues: 1310
  sheet:  None (None), residues: 0
  loop : -0.60 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 184 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.014   0.001   PHE C 413 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.002   0.000   ARG A 355 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  208 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7974 (mttt) cc_final: 0.7677 (mtpt)
REVERT: A  428 MET cc_start: 0.8187 (mmt) cc_final: 0.7699 (mmp)
REVERT: A  430 MET cc_start: 0.8189 (mtt) cc_final: 0.7907 (mtt)
REVERT: B  112 TRP cc_start: 0.6225 (t60) cc_final: 0.5747 (t-100)
REVERT: B  158 GLU cc_start: 0.7170 (pm20) cc_final: 0.6571 (pm20)
REVERT: B  184 TRP cc_start: 0.8147 (m-10) cc_final: 0.7939 (m-10)
REVERT: B  370 MET cc_start: 0.8028 (mtm) cc_final: 0.7569 (mtp)
REVERT: B  503 MET cc_start: 0.8993 (mtp) cc_final: 0.8583 (mtp)
REVERT: B  598 MET cc_start: 0.7591 (tpt) cc_final: 0.7081 (tpt)
REVERT: C  219 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7975 (mp)
REVERT: C  257 MET cc_start: 0.6911 (ptt) cc_final: 0.6546 (ptp)
  outliers start: 17
  outliers final: 13
  residues processed: 206
  average time/residue: 0.4248
  time to fit residues: 136.9961
Evaluate side-chains
  201 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 187
  time to evaluate  : 1.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 LEU
Chi-restraints excluded: chain C residue  228 THR
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Chi-restraints excluded: chain C residue  506 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   chunk 14 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 139 optimal weight:    3.9990
   chunk 146 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12660  Z= 0.138
  Angle     :  0.424   4.927  17229  Z= 0.222
  Chirality :  0.034   0.131   1991
  Planarity :  0.003   0.050   2089
  Dihedral  :  7.138  78.515   1827
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 12.69 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.37 (0.22), residues: 1593
  helix:  2.77 (0.15), residues: 1316
  sheet:  None (None), residues: 0
  loop : -0.60 (0.35), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 184 
 HIS   0.002   0.000   HIS B 394 
 PHE   0.010   0.001   PHE C 413 
 TYR   0.009   0.001   TYR A 357 
 ARG   0.001   0.000   ARG C 251 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 2.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7960 (mttt) cc_final: 0.7706 (mtpt)
REVERT: A  430 MET cc_start: 0.8135 (mtt) cc_final: 0.7849 (mtt)
REVERT: A  613 CYS cc_start: 0.7018 (m) cc_final: 0.6695 (m)
REVERT: B  158 GLU cc_start: 0.7238 (pm20) cc_final: 0.6643 (pm20)
REVERT: B  370 MET cc_start: 0.7905 (mtm) cc_final: 0.7607 (mtp)
REVERT: B  598 MET cc_start: 0.7440 (tpt) cc_final: 0.6923 (tpt)
REVERT: C  257 MET cc_start: 0.6844 (ptt) cc_final: 0.6496 (ptp)
  outliers start: 13
  outliers final: 10
  residues processed: 213
  average time/residue: 0.4451
  time to fit residues: 146.3382
Evaluate side-chains
  206 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 196
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 133 optimal weight:    0.5980
   chunk 142 optimal weight:    1.9990
   chunk 146 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 129 optimal weight:    0.3980
   chunk 135 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 151 optimal weight:    2.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12660  Z= 0.185
  Angle     :  0.443   5.240  17229  Z= 0.234
  Chirality :  0.035   0.134   1991
  Planarity :  0.003   0.048   2089
  Dihedral  :  7.172  79.250   1827
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 13.41 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.22), residues: 1593
  helix:  2.78 (0.15), residues: 1308
  sheet:  None (None), residues: 0
  loop : -0.45 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 184 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.013   0.001   PHE C 413 
 TYR   0.011   0.001   TYR A 357 
 ARG   0.001   0.000   ARG A 355 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  204 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 194
  time to evaluate  : 1.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.8004 (mttt) cc_final: 0.7724 (mtpt)
REVERT: A  430 MET cc_start: 0.8179 (mtt) cc_final: 0.7887 (mtt)
REVERT: A  503 MET cc_start: 0.8646 (mtm) cc_final: 0.8410 (mtm)
REVERT: A  613 CYS cc_start: 0.7109 (m) cc_final: 0.6793 (m)
REVERT: B  112 TRP cc_start: 0.6198 (t60) cc_final: 0.5968 (t-100)
REVERT: B  158 GLU cc_start: 0.7191 (pm20) cc_final: 0.6635 (pm20)
REVERT: B  370 MET cc_start: 0.7947 (mtm) cc_final: 0.7664 (mtp)
REVERT: B  598 MET cc_start: 0.7553 (tpt) cc_final: 0.7086 (tpt)
REVERT: C  257 MET cc_start: 0.7045 (ptt) cc_final: 0.6702 (ptp)
  outliers start: 10
  outliers final: 10
  residues processed: 203
  average time/residue: 0.4270
  time to fit residues: 133.4953
Evaluate side-chains
  202 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 158 optimal weight:    0.8980
   chunk 145 optimal weight:    2.9990
   chunk 126 optimal weight:    0.0030
   chunk 13 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    1.1394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12660  Z= 0.182
  Angle     :  0.441   5.405  17229  Z= 0.232
  Chirality :  0.035   0.135   1991
  Planarity :  0.003   0.050   2089
  Dihedral  :  7.146  79.135   1827
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.57 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.22), residues: 1593
  helix:  2.79 (0.15), residues: 1308
  sheet:  None (None), residues: 0
  loop : -0.46 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 184 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.013   0.001   PHE C 413 
 TYR   0.010   0.001   TYR A 357 
 ARG   0.001   0.000   ARG A 436 

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue THR  105 is missing expected H atoms. Skipping.
Residue LEU  107 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue ILE  110 is missing expected H atoms. Skipping.
Residue ILE  114 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Evaluate side-chains
  209 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 197
  time to evaluate  : 1.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7988 (mttt) cc_final: 0.7709 (mtpt)
REVERT: A  430 MET cc_start: 0.8186 (mtt) cc_final: 0.7911 (mtt)
REVERT: A  503 MET cc_start: 0.8636 (mtm) cc_final: 0.8387 (mtm)
REVERT: A  613 CYS cc_start: 0.7133 (m) cc_final: 0.6794 (m)
REVERT: B  370 MET cc_start: 0.7941 (mtm) cc_final: 0.7665 (mtp)
REVERT: B  598 MET cc_start: 0.7548 (tpt) cc_final: 0.7081 (tpt)
REVERT: C  257 MET cc_start: 0.7042 (ptt) cc_final: 0.6694 (ptp)
REVERT: C  413 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8316 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 208
  average time/residue: 0.4478
  time to fit residues: 143.6449
Evaluate side-chains
  206 residues out of total 1335 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 195
  time to evaluate  : 1.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  437 ASN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  578 VAL
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  447 SER
Chi-restraints excluded: chain C residue  448 SER
Chi-restraints excluded: chain C residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 116 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.142097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108494 restraints weight = 41794.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.91
r_work: 0.3143 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12660  Z= 0.175
  Angle     :  0.440   5.656  17229  Z= 0.231
  Chirality :  0.034   0.133   1991
  Planarity :  0.003   0.050   2089
  Dihedral  :  7.064  78.594   1827
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.65 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.45 (0.22), residues: 1593
  helix:  2.80 (0.15), residues: 1312
  sheet:  None (None), residues: 0
  loop : -0.38 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 184 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.012   0.001   PHE C 413 
 TYR   0.010   0.001   TYR A 357 
 ARG   0.002   0.000   ARG A 355 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4976.05 seconds
wall clock time: 87 minutes 31.16 seconds (5251.16 seconds total)