Starting phenix.real_space_refine on Sat Apr 6 15:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jol_36459/04_2024/8jol_36459_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.002 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 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5388 2.51 5 N 1439 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3965 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 3 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 445 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.58 Number of scatterers: 8513 At special positions: 0 Unit cell: (95.04, 114.84, 137.28, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1620 8.00 N 1439 7.00 C 5388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 3 sheets defined 55.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 32 removed outlier: 4.419A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.833A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 134 through 147 removed outlier: 3.952A pdb=" N MET A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 199 through 211 removed outlier: 4.023A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.692A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 263 removed outlier: 3.653A pdb=" N ALA A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.885A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 374 through 383 removed outlier: 4.498A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.654A pdb=" N PHE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 3.768A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 removed outlier: 4.526A pdb=" N LYS A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.630A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 4.377A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 Processing helix chain 'B' and resid 50 through 64 removed outlier: 3.541A pdb=" N ARG B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 81 through 95 removed outlier: 3.836A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.891A pdb=" N MET B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.897A pdb=" N MET B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.015A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.929A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.591A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.890A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 345 through 362 removed outlier: 3.791A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 383 removed outlier: 4.531A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.533A pdb=" N ALA B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 No H-bonds generated for 'chain 'B' and resid 408 through 411' Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.793A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 removed outlier: 4.491A pdb=" N LYS B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 4.065A pdb=" N ILE C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N MET C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 4.378A pdb=" N GLU C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.973A pdb=" N ALA C 75 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 76 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.837A pdb=" N GLU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 285 through 290 removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 272 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER A 186 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL A 248 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A 188 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASP A 250 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 190 " --> pdb=" O ASP A 250 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 252 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= C, first strand: chain 'B' and resid 286 through 290 removed outlier: 3.635A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER B 186 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 248 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 188 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP B 250 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU B 190 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL B 252 " --> pdb=" O LEU B 190 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2514 1.33 - 1.46: 1796 1.46 - 1.59: 4252 1.59 - 1.72: 6 1.72 - 1.85: 92 Bond restraints: 8660 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 8.95e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.480 -0.092 1.00e-02 1.00e+04 8.53e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.492 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP B 602 " pdb=" N7 ATP B 602 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.01e+01 bond pdb=" C8 ATP A 602 " pdb=" N7 ATP A 602 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 96.59 - 104.55: 161 104.55 - 112.51: 4239 112.51 - 120.47: 3971 120.47 - 128.43: 3308 128.43 - 136.39: 52 Bond angle restraints: 11731 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" N3 ATP B 602 " pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 127.04 136.39 -9.35 1.15e+00 7.59e-01 6.64e+01 ... (remaining 11726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4606 17.39 - 34.79: 480 34.79 - 52.18: 162 52.18 - 69.58: 78 69.58 - 86.97: 13 Dihedral angle restraints: 5339 sinusoidal: 2140 harmonic: 3199 Sorted by residual: dihedral pdb=" CA ASP B 216 " pdb=" C ASP B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP A 216 " pdb=" C ASP A 216 " pdb=" N LEU A 217 " pdb=" CA LEU A 217 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS A 268 " pdb=" C CYS A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 960 0.070 - 0.140: 301 0.140 - 0.210: 76 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS A 212 " pdb=" N LYS A 212 " pdb=" C LYS A 212 " pdb=" CB LYS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1357 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 87 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C VAL C 87 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL C 87 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 88 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 253 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 220 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 221 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.032 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1350 2.75 - 3.29: 9150 3.29 - 3.83: 14134 3.83 - 4.36: 18355 4.36 - 4.90: 27803 Nonbonded interactions: 70792 Sorted by model distance: nonbonded pdb=" O1B ATP A 602 " pdb=" O2G ATP A 602 " model vdw 2.214 3.040 nonbonded pdb=" O ARG A 259 " pdb=" N GLN A 262 " model vdw 2.275 2.520 nonbonded pdb=" O4' ATP A 602 " pdb=" O5' ATP A 602 " model vdw 2.319 2.432 nonbonded pdb=" OG SER B 166 " pdb="MG MG B 601 " model vdw 2.341 2.170 nonbonded pdb=" O LEU B 120 " pdb=" N ASN B 123 " model vdw 2.349 2.520 ... (remaining 70787 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 1 through 98 or resid 106 through 416 or resid 426 through \ 543 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.009 0.095 8660 Z= 0.591 Angle : 1.462 25.735 11731 Z= 1.023 Chirality : 0.074 0.349 1360 Planarity : 0.005 0.060 1502 Dihedral : 18.200 86.969 3243 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.32 % Favored : 86.83 % Rotamer: Outliers : 16.43 % Allowed : 15.21 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -4.77 (0.21), residues: 1071 helix: -3.29 (0.15), residues: 632 sheet: -2.60 (0.61), residues: 60 loop : -2.63 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.003 PHE A 156 TYR 0.022 0.004 TYR B 184 ARG 0.003 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 215 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8962 (m) cc_final: 0.8522 (p) REVERT: A 47 MET cc_start: 0.6707 (mmm) cc_final: 0.6151 (mmm) REVERT: A 123 ASN cc_start: 0.8269 (m110) cc_final: 0.7650 (t0) REVERT: A 128 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: A 144 LEU cc_start: 0.8740 (mt) cc_final: 0.8503 (mt) REVERT: A 185 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (t0) REVERT: A 205 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (m) REVERT: A 206 ASP cc_start: 0.8609 (m-30) cc_final: 0.8231 (m-30) REVERT: A 218 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 228 SER cc_start: 0.9145 (m) cc_final: 0.8888 (t) REVERT: A 233 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: A 286 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 290 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 443 LEU cc_start: 0.9052 (mt) cc_final: 0.8667 (mp) REVERT: B 45 SER cc_start: 0.4096 (OUTLIER) cc_final: 0.3860 (p) REVERT: B 128 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (OUTLIER) REVERT: B 185 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: B 190 LEU cc_start: 0.8856 (mt) cc_final: 0.8474 (mt) REVERT: B 218 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7944 (pt) REVERT: B 361 VAL cc_start: 0.8410 (t) cc_final: 0.7470 (p) REVERT: B 382 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7187 (t) outliers start: 149 outliers final: 10 residues processed: 317 average time/residue: 0.9508 time to fit residues: 325.3340 Evaluate side-chains 148 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 542 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 40 HIS A 123 ASN A 219 ASN A 329 ASN A 461 HIS A 471 GLN A 482 GLN A 534 GLN B 34 ASN B 56 ASN B 64 GLN B 76 ASN B 113 GLN B 244 ASN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN B 534 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8660 Z= 0.222 Angle : 0.749 11.467 11731 Z= 0.368 Chirality : 0.042 0.185 1360 Planarity : 0.005 0.054 1502 Dihedral : 11.574 81.441 1269 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.73 % Allowed : 25.58 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.24 (0.24), residues: 1071 helix: -1.23 (0.19), residues: 645 sheet: -2.33 (0.54), residues: 58 loop : -1.48 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 260 HIS 0.004 0.001 HIS A 225 PHE 0.020 0.002 PHE B 220 TYR 0.017 0.002 TYR A 77 ARG 0.010 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 118 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8953 (m) cc_final: 0.8718 (p) REVERT: A 63 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8313 (mmt-90) REVERT: A 198 LYS cc_start: 0.8924 (tppp) cc_final: 0.8528 (tppp) REVERT: A 206 ASP cc_start: 0.8465 (m-30) cc_final: 0.8190 (m-30) REVERT: A 218 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8652 (pt) REVERT: A 361 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.8796 (t) REVERT: A 364 GLU cc_start: 0.8365 (pm20) cc_final: 0.8098 (pm20) REVERT: A 383 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7959 (mm-30) REVERT: A 393 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8742 (tt) REVERT: A 486 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: B 114 MET cc_start: 0.7995 (mpt) cc_final: 0.7789 (mpt) REVERT: B 123 ASN cc_start: 0.8768 (t0) cc_final: 0.8465 (t0) REVERT: B 173 LEU cc_start: 0.9048 (mt) cc_final: 0.8821 (mm) REVERT: B 185 ASP cc_start: 0.8952 (m-30) cc_final: 0.8593 (m-30) REVERT: B 462 MET cc_start: 0.8639 (mpm) cc_final: 0.8396 (mpp) REVERT: B 533 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6338 (ppp) outliers start: 61 outliers final: 13 residues processed: 164 average time/residue: 0.9798 time to fit residues: 173.9267 Evaluate side-chains 121 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.0870 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 244 ASN A 536 HIS B 40 HIS B 64 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8660 Z= 0.221 Angle : 0.690 9.662 11731 Z= 0.336 Chirality : 0.041 0.142 1360 Planarity : 0.005 0.048 1502 Dihedral : 9.633 82.690 1236 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.29 % Allowed : 25.25 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.65 (0.26), residues: 1071 helix: 0.06 (0.21), residues: 640 sheet: -1.76 (0.61), residues: 56 loop : -0.86 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 410 HIS 0.003 0.001 HIS B 136 PHE 0.026 0.002 PHE B 395 TYR 0.015 0.001 TYR A 77 ARG 0.007 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 99 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6869 (tpt-90) REVERT: A 11 SER cc_start: 0.8998 (m) cc_final: 0.8695 (p) REVERT: A 47 MET cc_start: 0.7712 (mmm) cc_final: 0.6198 (mmm) REVERT: A 128 MET cc_start: 0.8888 (mtp) cc_final: 0.8410 (mtp) REVERT: A 198 LYS cc_start: 0.9001 (tppp) cc_final: 0.8562 (tppp) REVERT: A 206 ASP cc_start: 0.8602 (m-30) cc_final: 0.8367 (m-30) REVERT: A 307 MET cc_start: 0.8674 (tpp) cc_final: 0.8444 (tpp) REVERT: A 361 VAL cc_start: 0.9534 (OUTLIER) cc_final: 0.8947 (t) REVERT: A 364 GLU cc_start: 0.8281 (pm20) cc_final: 0.8057 (pm20) REVERT: A 486 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: B 114 MET cc_start: 0.8028 (mpt) cc_final: 0.7818 (mpt) REVERT: B 185 ASP cc_start: 0.9085 (m-30) cc_final: 0.8718 (m-30) REVERT: B 307 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.5846 (tpp) REVERT: B 364 GLU cc_start: 0.8064 (pm20) cc_final: 0.7859 (pm20) REVERT: B 432 ASP cc_start: 0.8539 (m-30) cc_final: 0.7826 (t0) outliers start: 48 outliers final: 11 residues processed: 136 average time/residue: 1.0387 time to fit residues: 152.1679 Evaluate side-chains 98 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 0.0570 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN B 56 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 1.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 8660 Z= 0.550 Angle : 0.883 12.019 11731 Z= 0.440 Chirality : 0.048 0.183 1360 Planarity : 0.006 0.067 1502 Dihedral : 10.553 77.830 1230 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.28 % Allowed : 26.02 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.88 (0.25), residues: 1071 helix: -0.11 (0.20), residues: 661 sheet: -1.88 (0.66), residues: 46 loop : -1.07 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 410 HIS 0.006 0.002 HIS A 19 PHE 0.026 0.002 PHE A 204 TYR 0.036 0.003 TYR B 369 ARG 0.007 0.001 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 76 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9407 (mm) REVERT: A 47 MET cc_start: 0.9006 (mmm) cc_final: 0.7682 (mmm) REVERT: A 52 GLU cc_start: 0.9308 (tt0) cc_final: 0.9079 (pp20) REVERT: A 71 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8605 (tm) REVERT: A 198 LYS cc_start: 0.9061 (tppp) cc_final: 0.8657 (tppp) REVERT: A 294 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8536 (pp20) REVERT: A 316 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: A 361 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9003 (t) REVERT: A 364 GLU cc_start: 0.8402 (pm20) cc_final: 0.8178 (pm20) REVERT: A 459 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.8925 (mm) REVERT: A 486 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 52 GLU cc_start: 0.9200 (mp0) cc_final: 0.8958 (mp0) REVERT: B 114 MET cc_start: 0.8841 (mpt) cc_final: 0.8615 (mpp) REVERT: B 459 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8881 (tt) outliers start: 57 outliers final: 8 residues processed: 121 average time/residue: 1.1788 time to fit residues: 152.5936 Evaluate side-chains 78 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 262 GLN A 475 ASN B 158 HIS ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 1.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8660 Z= 0.190 Angle : 0.664 12.256 11731 Z= 0.315 Chirality : 0.040 0.192 1360 Planarity : 0.005 0.053 1502 Dihedral : 8.928 81.279 1230 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.09 % Allowed : 28.56 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.02 (0.26), residues: 1071 helix: 0.72 (0.21), residues: 660 sheet: -1.45 (0.70), residues: 44 loop : -0.98 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 189 HIS 0.003 0.001 HIS B 82 PHE 0.014 0.001 PHE A 204 TYR 0.012 0.001 TYR B 135 ARG 0.006 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9078 (mmm) cc_final: 0.8207 (mmm) REVERT: A 198 LYS cc_start: 0.9004 (tppp) cc_final: 0.8565 (tppp) REVERT: A 307 MET cc_start: 0.9108 (tpp) cc_final: 0.8889 (mmm) REVERT: A 361 VAL cc_start: 0.9555 (OUTLIER) cc_final: 0.9121 (t) REVERT: A 364 GLU cc_start: 0.8337 (pm20) cc_final: 0.8125 (pm20) REVERT: A 459 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9129 (mm) REVERT: A 486 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: A 533 MET cc_start: 0.8810 (ppp) cc_final: 0.8564 (ppp) REVERT: B 49 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7385 (m) REVERT: B 52 GLU cc_start: 0.9052 (mp0) cc_final: 0.8724 (mp0) REVERT: B 114 MET cc_start: 0.8894 (mpt) cc_final: 0.8639 (mpp) REVERT: B 185 ASP cc_start: 0.9268 (m-30) cc_final: 0.8780 (m-30) REVERT: B 316 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8769 (pp20) REVERT: B 381 CYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9172 (m) REVERT: B 383 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8332 (mm-30) REVERT: B 435 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8881 (mtmm) REVERT: B 459 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8967 (tt) outliers start: 28 outliers final: 2 residues processed: 90 average time/residue: 1.2499 time to fit residues: 120.9192 Evaluate side-chains 69 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 283 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 1.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8660 Z= 0.180 Angle : 0.632 12.992 11731 Z= 0.298 Chirality : 0.039 0.175 1360 Planarity : 0.004 0.052 1502 Dihedral : 8.568 85.542 1230 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.76 % Allowed : 28.56 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.30 (0.26), residues: 1071 helix: 0.90 (0.21), residues: 668 sheet: -1.23 (0.69), residues: 46 loop : -0.82 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 410 HIS 0.003 0.001 HIS B 82 PHE 0.016 0.001 PHE A 204 TYR 0.018 0.001 TYR B 77 ARG 0.005 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 PHE cc_start: 0.8555 (t80) cc_final: 0.8311 (t80) REVERT: A 198 LYS cc_start: 0.8990 (tppp) cc_final: 0.8536 (tppp) REVERT: A 307 MET cc_start: 0.8981 (tpp) cc_final: 0.8750 (mmm) REVERT: A 361 VAL cc_start: 0.9581 (OUTLIER) cc_final: 0.9123 (t) REVERT: A 364 GLU cc_start: 0.8293 (pm20) cc_final: 0.8057 (pm20) REVERT: A 405 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8758 (pp) REVERT: A 459 ILE cc_start: 0.9550 (OUTLIER) cc_final: 0.9209 (mm) REVERT: A 486 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7454 (tm-30) REVERT: A 533 MET cc_start: 0.8688 (ppp) cc_final: 0.8385 (ppp) REVERT: B 49 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7353 (m) REVERT: B 52 GLU cc_start: 0.9110 (mp0) cc_final: 0.8808 (mp0) REVERT: B 114 MET cc_start: 0.8919 (mpt) cc_final: 0.8683 (mpp) REVERT: B 185 ASP cc_start: 0.9260 (m-30) cc_final: 0.8768 (m-30) REVERT: B 316 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (pp20) REVERT: B 383 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8441 (mm-30) REVERT: B 459 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8925 (tt) outliers start: 25 outliers final: 5 residues processed: 88 average time/residue: 1.1263 time to fit residues: 106.8791 Evaluate side-chains 74 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 1.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8660 Z= 0.186 Angle : 0.646 14.505 11731 Z= 0.301 Chirality : 0.039 0.175 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.450 88.209 1230 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.98 % Allowed : 27.78 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.26), residues: 1071 helix: 0.95 (0.21), residues: 677 sheet: -0.77 (0.72), residues: 46 loop : -0.76 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 410 HIS 0.004 0.000 HIS B 82 PHE 0.022 0.001 PHE A 220 TYR 0.017 0.001 TYR B 77 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.8979 (tppp) cc_final: 0.8520 (tppp) REVERT: A 307 MET cc_start: 0.9021 (tpp) cc_final: 0.8712 (mmm) REVERT: A 316 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: A 361 VAL cc_start: 0.9595 (OUTLIER) cc_final: 0.9147 (t) REVERT: A 364 GLU cc_start: 0.8241 (pm20) cc_final: 0.7980 (pm20) REVERT: A 376 MET cc_start: 0.9158 (mpm) cc_final: 0.8899 (mpp) REVERT: A 405 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8742 (pp) REVERT: A 459 ILE cc_start: 0.9558 (OUTLIER) cc_final: 0.9236 (mm) REVERT: A 533 MET cc_start: 0.8596 (ppp) cc_final: 0.8387 (ppp) REVERT: B 52 GLU cc_start: 0.9160 (mp0) cc_final: 0.8809 (mp0) REVERT: B 114 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8660 (mpp) REVERT: B 383 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8383 (mm-30) outliers start: 27 outliers final: 6 residues processed: 80 average time/residue: 1.1286 time to fit residues: 97.6942 Evaluate side-chains 71 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 1.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8660 Z= 0.259 Angle : 0.677 13.441 11731 Z= 0.317 Chirality : 0.041 0.191 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.542 86.615 1228 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.43 % Allowed : 28.11 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.55 (0.26), residues: 1071 helix: 0.99 (0.21), residues: 669 sheet: -0.42 (0.73), residues: 46 loop : -0.61 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 189 HIS 0.005 0.001 HIS B 225 PHE 0.021 0.001 PHE A 204 TYR 0.017 0.001 TYR B 77 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9554 (mm) cc_final: 0.9256 (tm) REVERT: A 198 LYS cc_start: 0.9029 (tppp) cc_final: 0.8538 (tppp) REVERT: A 316 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: A 361 VAL cc_start: 0.9597 (OUTLIER) cc_final: 0.9127 (t) REVERT: A 364 GLU cc_start: 0.8385 (pm20) cc_final: 0.8069 (pm20) REVERT: A 376 MET cc_start: 0.9230 (mpm) cc_final: 0.8950 (mpp) REVERT: A 405 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8854 (pp) REVERT: A 459 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9198 (mm) REVERT: A 533 MET cc_start: 0.8704 (ppp) cc_final: 0.8433 (ppp) REVERT: B 49 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7757 (m) REVERT: B 52 GLU cc_start: 0.9181 (mp0) cc_final: 0.8907 (mp0) REVERT: B 114 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8552 (mpp) REVERT: B 383 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8705 (mm-30) outliers start: 22 outliers final: 5 residues processed: 74 average time/residue: 1.1356 time to fit residues: 90.7639 Evaluate side-chains 68 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 1.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8660 Z= 0.298 Angle : 0.692 13.734 11731 Z= 0.328 Chirality : 0.041 0.181 1360 Planarity : 0.005 0.054 1502 Dihedral : 8.654 87.167 1228 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 28.67 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.52 (0.26), residues: 1071 helix: 1.01 (0.21), residues: 662 sheet: -0.26 (0.71), residues: 46 loop : -0.71 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 PHE 0.022 0.002 PHE A 539 TYR 0.017 0.001 TYR B 369 ARG 0.004 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.9062 (tppp) cc_final: 0.8580 (tppp) REVERT: A 316 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: A 361 VAL cc_start: 0.9519 (OUTLIER) cc_final: 0.8869 (t) REVERT: A 364 GLU cc_start: 0.8393 (pm20) cc_final: 0.8061 (pm20) REVERT: A 376 MET cc_start: 0.9231 (mpm) cc_final: 0.8970 (mpp) REVERT: A 405 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8939 (pp) REVERT: A 459 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9121 (mm) REVERT: A 533 MET cc_start: 0.8690 (ppp) cc_final: 0.8385 (ppp) REVERT: B 49 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 52 GLU cc_start: 0.9167 (mp0) cc_final: 0.8844 (mp0) REVERT: B 114 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (mpp) REVERT: B 383 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8677 (mm-30) outliers start: 19 outliers final: 7 residues processed: 70 average time/residue: 1.1235 time to fit residues: 85.3656 Evaluate side-chains 67 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 0.0070 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 254 GLN B 379 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 1.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8660 Z= 0.180 Angle : 0.658 15.293 11731 Z= 0.305 Chirality : 0.040 0.175 1360 Planarity : 0.004 0.053 1502 Dihedral : 8.379 85.540 1228 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.54 % Allowed : 29.55 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.69 (0.27), residues: 1071 helix: 1.03 (0.21), residues: 667 sheet: 0.03 (0.72), residues: 46 loop : -0.43 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 410 HIS 0.004 0.001 HIS B 82 PHE 0.022 0.001 PHE A 110 TYR 0.015 0.001 TYR B 77 ARG 0.004 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 LYS cc_start: 0.9018 (tppp) cc_final: 0.8534 (tppp) REVERT: A 316 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8311 (pm20) REVERT: A 361 VAL cc_start: 0.9590 (OUTLIER) cc_final: 0.9121 (t) REVERT: A 364 GLU cc_start: 0.8311 (pm20) cc_final: 0.8021 (pm20) REVERT: A 459 ILE cc_start: 0.9620 (OUTLIER) cc_final: 0.9193 (mm) REVERT: B 49 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 52 GLU cc_start: 0.9190 (mp0) cc_final: 0.8902 (mp0) REVERT: B 114 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: B 383 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8660 (mm-30) outliers start: 14 outliers final: 3 residues processed: 66 average time/residue: 1.2269 time to fit residues: 87.4303 Evaluate side-chains 62 residues out of total 985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.0270 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044704 restraints weight = 35539.588| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.29 r_work: 0.2702 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 1.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8660 Z= 0.177 Angle : 0.663 15.653 11731 Z= 0.304 Chirality : 0.039 0.170 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.080 77.149 1228 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.54 % Allowed : 29.55 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.76 (0.27), residues: 1071 helix: 1.08 (0.22), residues: 666 sheet: 0.43 (0.72), residues: 46 loop : -0.45 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 410 HIS 0.005 0.001 HIS B 82 PHE 0.020 0.001 PHE A 110 TYR 0.016 0.001 TYR B 77 ARG 0.004 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3023.27 seconds wall clock time: 54 minutes 51.32 seconds (3291.32 seconds total)