Starting phenix.real_space_refine on Mon Mar 18 18:29:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gka_40181/03_2024/8gka_40181_updated.pdb" } resolution = 2.55 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= 0.001 sd= 0.128 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 33 5.49 5 S 124 5.16 5 Na 1 4.78 5 C 14361 2.51 5 N 3409 2.21 5 O 3884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21812 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "C" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "D" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5090 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 15, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 354 Unusual residues: {' NA': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 435 Unusual residues: {'POV': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 291 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 10.61, per 1000 atoms: 0.49 Number of scatterers: 21812 At special positions: 0 Unit cell: (164.628, 164.628, 129.12, 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 124 16.00 P 33 15.00 Na 1 11.00 O 3884 8.00 N 3409 7.00 C 14361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 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: 7.71 Conformation dependent library (CDL) restraints added in 3.0 seconds 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 56.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.586A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 460 Processing helix chain 'A' and resid 484 through 508 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 585 Processing helix chain 'A' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 460 Processing helix chain 'B' and resid 484 through 508 Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 3.693A pdb=" N MET B 562 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.897A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 306 Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 460 Processing helix chain 'C' and resid 484 through 508 Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET C 562 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 585 Processing helix chain 'C' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.587A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 344 through 351 removed outlier: 3.724A pdb=" N ALA D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.925A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.525A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 460 Processing helix chain 'D' and resid 484 through 508 Processing helix chain 'D' and resid 513 through 519 Processing helix chain 'D' and resid 521 through 541 removed outlier: 3.659A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 566 removed outlier: 3.694A pdb=" N MET D 562 " --> pdb=" O GLY D 558 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 585 Processing helix chain 'D' and resid 587 through 607 removed outlier: 3.614A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 636 Processing helix chain 'D' and resid 651 through 665 Processing helix chain 'D' and resid 669 through 685 removed outlier: 3.898A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.537A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 376 through 382 removed outlier: 3.546A pdb=" N ASP A 379 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS A 731 " --> pdb=" O GLY A 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY A 718 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP B 379 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 731 " --> pdb=" O GLY B 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY B 718 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 376 through 382 removed outlier: 3.547A pdb=" N ASP C 379 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS C 731 " --> pdb=" O GLY C 718 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLY C 718 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 376 through 382 removed outlier: 3.548A pdb=" N ASP D 379 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS D 731 " --> pdb=" O GLY D 718 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLY D 718 " --> pdb=" O CYS D 731 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2808 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: 5.76 Time building geometry restraints manager: 8.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3578 1.32 - 1.45: 5647 1.45 - 1.57: 12727 1.57 - 1.69: 66 1.69 - 1.81: 204 Bond restraints: 22222 Sorted by residual: bond pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP B 151 " pdb=" CB ASP B 151 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.36e-01 bond pdb=" CA ASP A 151 " pdb=" CB ASP A 151 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.77e-01 bond pdb=" CA ASP D 151 " pdb=" CB ASP D 151 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.69e-02 3.50e+03 5.38e-01 bond pdb=" CB PRO C 510 " pdb=" CG PRO C 510 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.36e-01 ... (remaining 22217 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.16: 248 104.16 - 111.62: 10154 111.62 - 119.09: 8083 119.09 - 126.56: 10998 126.56 - 134.03: 339 Bond angle restraints: 29822 Sorted by residual: angle pdb=" C HIS B 150 " pdb=" N ASP B 151 " pdb=" CA ASP B 151 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 121.54 128.20 -6.66 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C HIS A 150 " pdb=" N ASP A 151 " pdb=" CA ASP A 151 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" C HIS D 150 " pdb=" N ASP D 151 " pdb=" CA ASP D 151 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA LEU D 608 " pdb=" CB LEU D 608 " pdb=" CG LEU D 608 " ideal model delta sigma weight residual 116.30 124.29 -7.99 3.50e+00 8.16e-02 5.21e+00 ... (remaining 29817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12994 24.39 - 48.78: 433 48.78 - 73.18: 131 73.18 - 97.57: 17 97.57 - 121.96: 6 Dihedral angle restraints: 13581 sinusoidal: 6221 harmonic: 7360 Sorted by residual: dihedral pdb=" C27 POV B 803 " pdb=" C28 POV B 803 " pdb=" C29 POV B 803 " pdb="C210 POV B 803 " ideal model delta sinusoidal sigma weight residual 127.48 -110.56 -121.96 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C27 POV A 809 " pdb=" C28 POV A 809 " pdb=" C29 POV A 809 " pdb="C210 POV A 809 " ideal model delta sinusoidal sigma weight residual 127.48 -116.73 -115.79 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C3 POV B 808 " pdb=" C31 POV B 808 " pdb=" O31 POV B 808 " pdb=" C32 POV B 808 " ideal model delta sinusoidal sigma weight residual 172.61 -76.70 -110.69 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2038 0.024 - 0.047: 729 0.047 - 0.071: 342 0.071 - 0.095: 83 0.095 - 0.119: 41 Chirality restraints: 3233 Sorted by residual: chirality pdb=" CA ILE B 734 " pdb=" N ILE B 734 " pdb=" C ILE B 734 " pdb=" CB ILE B 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 734 " pdb=" N ILE D 734 " pdb=" C ILE D 734 " pdb=" CB ILE D 734 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 ... (remaining 3230 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO C 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 180 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO D 181 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 181 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 181 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 181 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.017 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5933 2.81 - 3.33: 21654 3.33 - 3.86: 36181 3.86 - 4.38: 44415 4.38 - 4.90: 74855 Nonbonded interactions: 183038 Sorted by model distance: nonbonded pdb=" O GLY B 638 " pdb="NA NA A 801 " model vdw 2.291 2.470 nonbonded pdb=" O GLY C 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY A 638 " pdb="NA NA A 801 " model vdw 2.292 2.470 nonbonded pdb=" O GLY D 638 " pdb="NA NA A 801 " model vdw 2.293 2.470 nonbonded pdb=" NZ LYS C 589 " pdb=" O14 POV C 805 " model vdw 2.297 2.520 ... (remaining 183033 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 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or resid 805 or (resid 806 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C3 or name C31 or name C32 or name C33 or name C34 or name O11 or nam \ e O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or resid 807)) selection = (chain 'B' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) selection = (chain 'D' and (resid 117 through 756 or (resid 802 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or \ name O22 or name O31 or name O32 or name P or name C210)) or (resid 803 and (nam \ e N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or na \ me C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P )) or (resid 804 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or \ name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 805 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210) \ ) or (resid 806 and (name N or name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or name C33 \ or name C34 or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O22 or name O31 or name O32 or name P )) or (resid 807 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.110 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 52.440 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.120 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:10.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.001 0.037 22222 Z= 0.092 Angle : 0.385 7.989 29822 Z= 0.190 Chirality : 0.032 0.119 3233 Planarity : 0.002 0.030 3600 Dihedral : 13.139 121.958 8793 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.79 % Favored : 95.67 % 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: 0.61 (0.17), residues: 2484 helix: 1.20 (0.13), residues: 1556 sheet: 3.44 (0.63), residues: 64 loop : -1.31 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 739 HIS 0.002 0.000 HIS C 301 PHE 0.004 0.001 PHE D 377 TYR 0.006 0.001 TYR D 208 ARG 0.002 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 460 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LYS cc_start: 0.7128 (mppt) cc_final: 0.6923 (mppt) REVERT: A 346 GLN cc_start: 0.8610 (mt0) cc_final: 0.7975 (mt0) REVERT: A 351 MET cc_start: 0.9254 (mtp) cc_final: 0.9013 (mtp) REVERT: A 514 GLN cc_start: 0.5620 (mm-40) cc_final: 0.5380 (tt0) REVERT: A 562 MET cc_start: 0.8987 (mmt) cc_final: 0.8652 (mmt) REVERT: B 253 LYS cc_start: 0.7125 (mppt) cc_final: 0.6922 (mppt) REVERT: B 346 GLN cc_start: 0.8626 (mt0) cc_final: 0.7990 (mt0) REVERT: B 351 MET cc_start: 0.9247 (mtp) cc_final: 0.9003 (mtp) REVERT: B 562 MET cc_start: 0.9015 (mmt) cc_final: 0.8728 (mmt) REVERT: B 680 THR cc_start: 0.8279 (p) cc_final: 0.8048 (m) REVERT: C 346 GLN cc_start: 0.8631 (mt0) cc_final: 0.7984 (mt0) REVERT: C 351 MET cc_start: 0.9252 (mtp) cc_final: 0.9010 (mtp) REVERT: C 562 MET cc_start: 0.9012 (mmt) cc_final: 0.8730 (mmt) REVERT: C 680 THR cc_start: 0.8274 (p) cc_final: 0.8054 (m) REVERT: D 346 GLN cc_start: 0.8630 (mt0) cc_final: 0.7996 (mt0) REVERT: D 351 MET cc_start: 0.9253 (mtp) cc_final: 0.9014 (mtp) REVERT: D 562 MET cc_start: 0.8992 (mmt) cc_final: 0.8687 (mmt) REVERT: D 680 THR cc_start: 0.8287 (p) cc_final: 0.8071 (m) outliers start: 12 outliers final: 4 residues processed: 468 average time/residue: 1.4004 time to fit residues: 738.0291 Evaluate side-chains 313 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 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 143 GLN A 197 ASN A 205 ASN A 279 GLN A 580 GLN A 645 GLN A 695 GLN B 279 GLN B 570 GLN B 580 GLN B 645 GLN B 647 ASN B 695 GLN C 143 GLN C 197 ASN C 279 GLN C 580 GLN C 645 GLN C 695 GLN D 143 GLN D 197 ASN D 279 GLN D 580 GLN D 645 GLN D 695 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22222 Z= 0.365 Angle : 0.676 12.263 29822 Z= 0.331 Chirality : 0.042 0.154 3233 Planarity : 0.005 0.040 3600 Dihedral : 17.084 135.951 3893 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.07 % Allowed : 10.42 % Favored : 86.51 % 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: 0.32 (0.16), residues: 2484 helix: 0.99 (0.12), residues: 1596 sheet: 2.95 (0.63), residues: 64 loop : -1.54 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 692 HIS 0.007 0.001 HIS D 301 PHE 0.015 0.002 PHE A 526 TYR 0.020 0.003 TYR B 321 ARG 0.005 0.001 ARG B 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 337 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.6791 (mmm) cc_final: 0.6189 (mmm) REVERT: A 185 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 378 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9025 (t) REVERT: A 562 MET cc_start: 0.9149 (mmt) cc_final: 0.8808 (mmt) REVERT: A 619 CYS cc_start: 0.6333 (p) cc_final: 0.6059 (p) REVERT: A 729 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7866 (mtt180) REVERT: A 738 LYS cc_start: 0.8256 (pttt) cc_final: 0.8021 (ptpp) REVERT: A 740 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7785 (p) REVERT: B 159 MET cc_start: 0.6745 (mmm) cc_final: 0.6037 (mmm) REVERT: B 185 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 378 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.9020 (t) REVERT: B 514 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6602 (mm-40) REVERT: B 562 MET cc_start: 0.9167 (mmt) cc_final: 0.8799 (mmt) REVERT: B 619 CYS cc_start: 0.6305 (p) cc_final: 0.6037 (p) REVERT: B 729 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7890 (mtt180) REVERT: B 738 LYS cc_start: 0.8277 (pttt) cc_final: 0.7938 (ptpp) REVERT: B 740 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7755 (p) REVERT: C 159 MET cc_start: 0.6906 (mmm) cc_final: 0.6187 (mmm) REVERT: C 185 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 378 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.9023 (t) REVERT: C 514 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6556 (mm-40) REVERT: C 562 MET cc_start: 0.9163 (mmt) cc_final: 0.8836 (mmt) REVERT: C 619 CYS cc_start: 0.6286 (p) cc_final: 0.6040 (p) REVERT: C 729 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7880 (mtt180) REVERT: C 738 LYS cc_start: 0.8265 (pttt) cc_final: 0.7933 (ptpp) REVERT: C 740 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7768 (p) REVERT: D 159 MET cc_start: 0.6743 (mmm) cc_final: 0.6071 (mmm) REVERT: D 185 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D 378 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.9020 (t) REVERT: D 514 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6484 (mm-40) REVERT: D 562 MET cc_start: 0.9137 (mmt) cc_final: 0.8816 (mmt) REVERT: D 619 CYS cc_start: 0.6289 (p) cc_final: 0.6048 (p) REVERT: D 687 GLU cc_start: 0.7852 (pt0) cc_final: 0.7476 (pp20) REVERT: D 729 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7882 (mtt180) REVERT: D 738 LYS cc_start: 0.8267 (pttt) cc_final: 0.7932 (ptpp) REVERT: D 740 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7749 (p) outliers start: 68 outliers final: 24 residues processed: 379 average time/residue: 1.4719 time to fit residues: 625.5978 Evaluate side-chains 326 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 287 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 621 SER Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain D residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 750 ASN B 143 GLN B 182 ASN B 197 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 750 ASN C 220 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 750 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22222 Z= 0.165 Angle : 0.514 11.245 29822 Z= 0.251 Chirality : 0.036 0.146 3233 Planarity : 0.003 0.027 3600 Dihedral : 16.489 123.044 3893 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.75 % 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: 0.63 (0.16), residues: 2484 helix: 1.27 (0.12), residues: 1592 sheet: 3.11 (0.62), residues: 64 loop : -1.51 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 692 HIS 0.006 0.001 HIS D 301 PHE 0.008 0.001 PHE A 526 TYR 0.016 0.002 TYR B 208 ARG 0.002 0.000 ARG B 729 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 310 time to evaluate : 2.361 Fit side-chains REVERT: A 159 MET cc_start: 0.6929 (mmm) cc_final: 0.6357 (mmm) REVERT: A 185 GLU cc_start: 0.7301 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 253 LYS cc_start: 0.7228 (mppt) cc_final: 0.6947 (mppt) REVERT: A 562 MET cc_start: 0.9173 (mmt) cc_final: 0.8658 (mmt) REVERT: A 619 CYS cc_start: 0.6263 (p) cc_final: 0.6007 (p) REVERT: A 729 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: A 738 LYS cc_start: 0.8075 (pttt) cc_final: 0.7834 (ptpp) REVERT: A 740 THR cc_start: 0.7953 (m) cc_final: 0.7600 (p) REVERT: A 743 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8134 (ptpp) REVERT: B 159 MET cc_start: 0.6800 (mmm) cc_final: 0.6095 (mmm) REVERT: B 185 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7096 (mm-30) REVERT: B 253 LYS cc_start: 0.7212 (mppt) cc_final: 0.6937 (mppt) REVERT: B 514 GLN cc_start: 0.7058 (tt0) cc_final: 0.6568 (mm-40) REVERT: B 562 MET cc_start: 0.9189 (mmt) cc_final: 0.8730 (mmt) REVERT: B 619 CYS cc_start: 0.6251 (p) cc_final: 0.5992 (p) REVERT: B 729 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7994 (mtp180) REVERT: B 738 LYS cc_start: 0.8165 (pttt) cc_final: 0.7788 (ptpp) REVERT: B 740 THR cc_start: 0.7975 (m) cc_final: 0.7611 (p) REVERT: C 159 MET cc_start: 0.7016 (mmm) cc_final: 0.6248 (mmm) REVERT: C 185 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7094 (mm-30) REVERT: C 514 GLN cc_start: 0.6990 (tt0) cc_final: 0.6527 (mm-40) REVERT: C 562 MET cc_start: 0.9182 (mmt) cc_final: 0.8695 (mmt) REVERT: C 619 CYS cc_start: 0.6243 (p) cc_final: 0.6003 (p) REVERT: C 687 GLU cc_start: 0.7722 (pt0) cc_final: 0.7337 (pp20) REVERT: C 729 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7991 (mtp180) REVERT: C 738 LYS cc_start: 0.8154 (pttt) cc_final: 0.7778 (ptpp) REVERT: C 740 THR cc_start: 0.7815 (m) cc_final: 0.7461 (p) REVERT: D 185 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7129 (mm-30) REVERT: D 514 GLN cc_start: 0.6975 (tt0) cc_final: 0.6482 (mm-40) REVERT: D 562 MET cc_start: 0.9151 (mmt) cc_final: 0.8649 (mmt) REVERT: D 619 CYS cc_start: 0.6252 (p) cc_final: 0.6011 (p) REVERT: D 687 GLU cc_start: 0.7740 (pt0) cc_final: 0.7396 (pp20) REVERT: D 729 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7983 (mtp180) REVERT: D 738 LYS cc_start: 0.8156 (pttt) cc_final: 0.7780 (ptpp) REVERT: D 740 THR cc_start: 0.7953 (m) cc_final: 0.7600 (p) outliers start: 60 outliers final: 12 residues processed: 362 average time/residue: 1.5338 time to fit residues: 620.5552 Evaluate side-chains 309 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 293 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 729 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 647 ASN A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 750 ASN C 279 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 750 ASN D 279 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 GLN D 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22222 Z= 0.173 Angle : 0.517 10.734 29822 Z= 0.253 Chirality : 0.036 0.143 3233 Planarity : 0.003 0.028 3600 Dihedral : 16.101 117.482 3885 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.44 % Allowed : 14.49 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.16), residues: 2484 helix: 1.38 (0.12), residues: 1600 sheet: 3.24 (0.63), residues: 64 loop : -1.56 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 710 HIS 0.006 0.001 HIS D 301 PHE 0.010 0.001 PHE A 506 TYR 0.014 0.002 TYR D 208 ARG 0.002 0.000 ARG B 729 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 306 time to evaluate : 2.664 Fit side-chains REVERT: A 185 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6956 (mm-30) REVERT: A 188 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.7182 (mtm-85) REVERT: A 253 LYS cc_start: 0.7218 (mppt) cc_final: 0.6950 (mppt) REVERT: A 562 MET cc_start: 0.9184 (mmt) cc_final: 0.8670 (mmt) REVERT: A 619 CYS cc_start: 0.6183 (p) cc_final: 0.5944 (p) REVERT: A 729 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7869 (mtp180) REVERT: A 736 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: A 738 LYS cc_start: 0.8102 (pttt) cc_final: 0.7828 (ptpp) REVERT: A 740 THR cc_start: 0.8008 (m) cc_final: 0.7736 (p) REVERT: A 743 LYS cc_start: 0.8343 (ptpp) cc_final: 0.8114 (ptpp) REVERT: B 159 MET cc_start: 0.6950 (mmm) cc_final: 0.6313 (mmm) REVERT: B 185 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 253 LYS cc_start: 0.7216 (mppt) cc_final: 0.6947 (mppt) REVERT: B 514 GLN cc_start: 0.7155 (tt0) cc_final: 0.6645 (mm-40) REVERT: B 562 MET cc_start: 0.9199 (mmt) cc_final: 0.8742 (mmt) REVERT: B 619 CYS cc_start: 0.6167 (p) cc_final: 0.5915 (p) REVERT: B 687 GLU cc_start: 0.7728 (pt0) cc_final: 0.7466 (pp20) REVERT: B 729 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7877 (mtp180) REVERT: B 736 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 738 LYS cc_start: 0.8098 (pttt) cc_final: 0.7832 (ptpp) REVERT: B 740 THR cc_start: 0.7962 (m) cc_final: 0.7659 (p) REVERT: C 159 MET cc_start: 0.7032 (mmm) cc_final: 0.6449 (mmm) REVERT: C 185 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6909 (mm-30) REVERT: C 283 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: C 514 GLN cc_start: 0.7065 (tt0) cc_final: 0.6579 (mm-40) REVERT: C 562 MET cc_start: 0.9185 (mmt) cc_final: 0.8689 (mmt) REVERT: C 619 CYS cc_start: 0.6157 (p) cc_final: 0.5923 (p) REVERT: C 687 GLU cc_start: 0.7704 (pt0) cc_final: 0.7345 (pp20) REVERT: C 729 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7875 (mtp180) REVERT: C 736 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: C 738 LYS cc_start: 0.8086 (pttt) cc_final: 0.7823 (ptpp) REVERT: C 740 THR cc_start: 0.7966 (m) cc_final: 0.7671 (p) REVERT: D 159 MET cc_start: 0.7091 (mmm) cc_final: 0.6467 (mmm) REVERT: D 185 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6980 (mm-30) REVERT: D 514 GLN cc_start: 0.7001 (tt0) cc_final: 0.6505 (mm-40) REVERT: D 562 MET cc_start: 0.9162 (mmt) cc_final: 0.8652 (mmt) REVERT: D 619 CYS cc_start: 0.6166 (p) cc_final: 0.5937 (p) REVERT: D 729 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7870 (mtp180) REVERT: D 736 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: D 738 LYS cc_start: 0.8086 (pttt) cc_final: 0.7824 (ptpp) REVERT: D 740 THR cc_start: 0.7963 (m) cc_final: 0.7655 (p) outliers start: 54 outliers final: 14 residues processed: 347 average time/residue: 1.5857 time to fit residues: 613.5773 Evaluate side-chains 305 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 282 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 736 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 736 GLU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 220 ASN A 279 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN B 182 ASN B 220 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 750 ASN C 279 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 750 ASN D 182 ASN D 580 GLN D 750 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 22222 Z= 0.360 Angle : 0.667 12.327 29822 Z= 0.323 Chirality : 0.042 0.169 3233 Planarity : 0.004 0.039 3600 Dihedral : 16.949 118.198 3885 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.70 % Allowed : 13.58 % Favored : 82.72 % 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: 0.36 (0.16), residues: 2484 helix: 0.92 (0.12), residues: 1616 sheet: 2.60 (0.63), residues: 64 loop : -1.30 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 710 HIS 0.010 0.002 HIS A 301 PHE 0.011 0.002 PHE C 542 TYR 0.018 0.003 TYR C 208 ARG 0.004 0.001 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 310 time to evaluate : 2.455 Fit side-chains REVERT: A 185 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 253 LYS cc_start: 0.7199 (mppt) cc_final: 0.6940 (mppt) REVERT: A 283 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: A 411 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 447 PHE cc_start: 0.8617 (m-80) cc_final: 0.8406 (m-10) REVERT: A 488 MET cc_start: 0.6727 (mmt) cc_final: 0.6454 (mtm) REVERT: A 562 MET cc_start: 0.9193 (mmt) cc_final: 0.8855 (mmt) REVERT: A 619 CYS cc_start: 0.6256 (p) cc_final: 0.6014 (p) REVERT: A 729 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7903 (mtt180) REVERT: A 738 LYS cc_start: 0.8140 (pttt) cc_final: 0.7848 (ptpp) REVERT: A 740 THR cc_start: 0.7962 (m) cc_final: 0.7711 (p) REVERT: B 159 MET cc_start: 0.6806 (mmm) cc_final: 0.6100 (mmm) REVERT: B 185 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 253 LYS cc_start: 0.7189 (mppt) cc_final: 0.6928 (mppt) REVERT: B 411 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7492 (p) REVERT: B 488 MET cc_start: 0.6726 (mmt) cc_final: 0.6447 (mtm) REVERT: B 514 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6621 (mm-40) REVERT: B 562 MET cc_start: 0.9181 (mmt) cc_final: 0.8851 (mmt) REVERT: B 619 CYS cc_start: 0.6242 (p) cc_final: 0.5996 (p) REVERT: B 729 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7913 (mtt180) REVERT: B 738 LYS cc_start: 0.8154 (pttt) cc_final: 0.7799 (ptpp) REVERT: B 740 THR cc_start: 0.7993 (m) cc_final: 0.7716 (p) REVERT: C 159 MET cc_start: 0.7005 (mmm) cc_final: 0.6325 (mmm) REVERT: C 185 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 283 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7544 (mt-10) REVERT: C 411 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7491 (p) REVERT: C 488 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6415 (mtm) REVERT: C 514 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6599 (mm-40) REVERT: C 562 MET cc_start: 0.9176 (mmt) cc_final: 0.8831 (mmt) REVERT: C 619 CYS cc_start: 0.6261 (p) cc_final: 0.6031 (p) REVERT: C 729 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.7915 (mtt180) REVERT: C 738 LYS cc_start: 0.8140 (pttt) cc_final: 0.7789 (ptpp) REVERT: C 740 THR cc_start: 0.7979 (m) cc_final: 0.7698 (p) REVERT: D 185 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7067 (mm-30) REVERT: D 280 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 411 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7518 (p) REVERT: D 447 PHE cc_start: 0.8620 (m-80) cc_final: 0.8408 (m-10) REVERT: D 488 MET cc_start: 0.6758 (mmt) cc_final: 0.6484 (mtm) REVERT: D 514 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6567 (mm-40) REVERT: D 562 MET cc_start: 0.9149 (mmt) cc_final: 0.8817 (mmt) REVERT: D 619 CYS cc_start: 0.6233 (p) cc_final: 0.6009 (p) REVERT: D 729 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7908 (mtt180) REVERT: D 738 LYS cc_start: 0.8137 (pttt) cc_final: 0.7787 (ptpp) REVERT: D 740 THR cc_start: 0.7991 (m) cc_final: 0.7711 (p) outliers start: 82 outliers final: 30 residues processed: 370 average time/residue: 1.5756 time to fit residues: 652.0141 Evaluate side-chains 342 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 SER Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 514 GLN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 729 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 59 optimal weight: 0.0670 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 125 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 279 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 182 ASN ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22222 Z= 0.163 Angle : 0.528 10.927 29822 Z= 0.258 Chirality : 0.036 0.154 3233 Planarity : 0.003 0.030 3600 Dihedral : 16.278 118.973 3885 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.03 % Allowed : 15.97 % Favored : 81.99 % 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: 0.56 (0.16), residues: 2484 helix: 1.14 (0.12), residues: 1632 sheet: 2.51 (0.60), residues: 64 loop : -1.43 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 710 HIS 0.006 0.001 HIS C 301 PHE 0.013 0.001 PHE D 506 TYR 0.015 0.001 TYR A 208 ARG 0.002 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 306 time to evaluate : 2.614 Fit side-chains REVERT: A 185 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 253 LYS cc_start: 0.7175 (mppt) cc_final: 0.6933 (mppt) REVERT: A 447 PHE cc_start: 0.8598 (m-80) cc_final: 0.8381 (m-10) REVERT: A 488 MET cc_start: 0.6676 (mmt) cc_final: 0.6351 (mtm) REVERT: A 562 MET cc_start: 0.9185 (mmt) cc_final: 0.8705 (mmt) REVERT: A 619 CYS cc_start: 0.6136 (p) cc_final: 0.5899 (p) REVERT: A 687 GLU cc_start: 0.7735 (pt0) cc_final: 0.7410 (pp20) REVERT: A 729 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8047 (mtp180) REVERT: A 738 LYS cc_start: 0.8091 (pttt) cc_final: 0.7808 (pttm) REVERT: A 740 THR cc_start: 0.8027 (m) cc_final: 0.7736 (p) REVERT: B 159 MET cc_start: 0.6854 (mmm) cc_final: 0.6283 (mmm) REVERT: B 185 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 253 LYS cc_start: 0.7131 (mppt) cc_final: 0.6893 (mppt) REVERT: B 280 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8435 (tp) REVERT: B 488 MET cc_start: 0.6601 (mmt) cc_final: 0.6253 (mtm) REVERT: B 514 GLN cc_start: 0.7025 (tt0) cc_final: 0.6441 (mm-40) REVERT: B 562 MET cc_start: 0.9204 (mmt) cc_final: 0.8774 (mmt) REVERT: B 619 CYS cc_start: 0.6153 (p) cc_final: 0.5919 (p) REVERT: B 687 GLU cc_start: 0.7752 (pt0) cc_final: 0.7508 (pp20) REVERT: B 738 LYS cc_start: 0.8129 (pttt) cc_final: 0.7824 (ptpp) REVERT: B 740 THR cc_start: 0.7939 (m) cc_final: 0.7629 (p) REVERT: C 159 MET cc_start: 0.6942 (mmm) cc_final: 0.6069 (mmm) REVERT: C 185 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7083 (mm-30) REVERT: C 280 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8443 (tp) REVERT: C 351 MET cc_start: 0.9230 (mtp) cc_final: 0.9026 (mtp) REVERT: C 488 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6257 (mtm) REVERT: C 514 GLN cc_start: 0.6980 (tt0) cc_final: 0.6429 (mm-40) REVERT: C 562 MET cc_start: 0.9194 (mmt) cc_final: 0.8717 (mmt) REVERT: C 619 CYS cc_start: 0.6169 (p) cc_final: 0.5933 (p) REVERT: C 687 GLU cc_start: 0.7734 (pt0) cc_final: 0.7480 (pp20) REVERT: C 738 LYS cc_start: 0.8119 (pttt) cc_final: 0.7816 (ptpp) REVERT: C 740 THR cc_start: 0.7937 (m) cc_final: 0.7626 (p) REVERT: D 159 MET cc_start: 0.7094 (mmm) cc_final: 0.6152 (mmm) REVERT: D 185 GLU cc_start: 0.7232 (mm-30) cc_final: 0.7006 (mm-30) REVERT: D 280 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8439 (tp) REVERT: D 447 PHE cc_start: 0.8631 (m-80) cc_final: 0.8422 (m-10) REVERT: D 488 MET cc_start: 0.6631 (mmt) cc_final: 0.6293 (mtm) REVERT: D 514 GLN cc_start: 0.6988 (tt0) cc_final: 0.6529 (mm-40) REVERT: D 562 MET cc_start: 0.9160 (mmt) cc_final: 0.8671 (mmt) REVERT: D 619 CYS cc_start: 0.6141 (p) cc_final: 0.5914 (p) REVERT: D 738 LYS cc_start: 0.8121 (pttt) cc_final: 0.7819 (ptpp) REVERT: D 740 THR cc_start: 0.7935 (m) cc_final: 0.7621 (p) outliers start: 45 outliers final: 17 residues processed: 342 average time/residue: 1.5466 time to fit residues: 591.6132 Evaluate side-chains 317 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 295 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 279 GLN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 220 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22222 Z= 0.187 Angle : 0.542 10.616 29822 Z= 0.263 Chirality : 0.037 0.146 3233 Planarity : 0.003 0.030 3600 Dihedral : 16.181 116.911 3885 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.12 % Allowed : 16.16 % Favored : 81.72 % 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: 0.64 (0.16), residues: 2484 helix: 1.20 (0.12), residues: 1628 sheet: 2.56 (0.60), residues: 64 loop : -1.37 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 710 HIS 0.006 0.001 HIS A 301 PHE 0.010 0.001 PHE C 316 TYR 0.014 0.002 TYR A 208 ARG 0.002 0.000 ARG B 729 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 306 time to evaluate : 2.295 Fit side-chains REVERT: A 185 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 253 LYS cc_start: 0.7164 (mppt) cc_final: 0.6923 (mppt) REVERT: A 447 PHE cc_start: 0.8599 (m-80) cc_final: 0.8380 (m-10) REVERT: A 485 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6270 (tp) REVERT: A 488 MET cc_start: 0.6663 (mmt) cc_final: 0.6319 (mtm) REVERT: A 562 MET cc_start: 0.9187 (mmt) cc_final: 0.8688 (mmt) REVERT: A 619 CYS cc_start: 0.6095 (p) cc_final: 0.5862 (p) REVERT: A 687 GLU cc_start: 0.7749 (pt0) cc_final: 0.7398 (pp20) REVERT: A 729 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7849 (mtp180) REVERT: A 738 LYS cc_start: 0.8081 (pttt) cc_final: 0.7825 (pttm) REVERT: A 740 THR cc_start: 0.8022 (m) cc_final: 0.7744 (p) REVERT: B 159 MET cc_start: 0.6928 (mmm) cc_final: 0.6203 (mmm) REVERT: B 185 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 253 LYS cc_start: 0.7157 (mppt) cc_final: 0.6916 (mppt) REVERT: B 280 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 369 ARG cc_start: 0.7105 (tmm160) cc_final: 0.6900 (tmm160) REVERT: B 488 MET cc_start: 0.6582 (mmt) cc_final: 0.6301 (mtm) REVERT: B 514 GLN cc_start: 0.6974 (tt0) cc_final: 0.6422 (mm-40) REVERT: B 562 MET cc_start: 0.9212 (mmt) cc_final: 0.8769 (mmt) REVERT: B 619 CYS cc_start: 0.6153 (p) cc_final: 0.5904 (p) REVERT: B 738 LYS cc_start: 0.8109 (pttt) cc_final: 0.7811 (ptpp) REVERT: B 740 THR cc_start: 0.7951 (m) cc_final: 0.7668 (p) REVERT: C 159 MET cc_start: 0.6978 (mmm) cc_final: 0.6123 (mmm) REVERT: C 185 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 283 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: C 369 ARG cc_start: 0.7107 (tmm160) cc_final: 0.6898 (tmm160) REVERT: C 488 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6266 (mtm) REVERT: C 514 GLN cc_start: 0.6965 (tt0) cc_final: 0.6430 (mm-40) REVERT: C 562 MET cc_start: 0.9207 (mmt) cc_final: 0.8721 (mmt) REVERT: C 619 CYS cc_start: 0.6149 (p) cc_final: 0.5916 (p) REVERT: C 687 GLU cc_start: 0.7744 (pt0) cc_final: 0.7476 (pp20) REVERT: C 738 LYS cc_start: 0.8096 (pttt) cc_final: 0.7803 (ptpp) REVERT: C 740 THR cc_start: 0.7936 (m) cc_final: 0.7651 (p) REVERT: D 159 MET cc_start: 0.7172 (mmm) cc_final: 0.6204 (mmm) REVERT: D 185 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6990 (mm-30) REVERT: D 280 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8461 (tp) REVERT: D 369 ARG cc_start: 0.7106 (tmm160) cc_final: 0.6901 (tmm160) REVERT: D 447 PHE cc_start: 0.8630 (m-80) cc_final: 0.8420 (m-10) REVERT: D 485 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6314 (tp) REVERT: D 488 MET cc_start: 0.6611 (mmt) cc_final: 0.6340 (mtm) REVERT: D 514 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6568 (mm-40) REVERT: D 562 MET cc_start: 0.9163 (mmt) cc_final: 0.8660 (mmt) REVERT: D 619 CYS cc_start: 0.6125 (p) cc_final: 0.5896 (p) REVERT: D 738 LYS cc_start: 0.8099 (pttt) cc_final: 0.7806 (ptpp) REVERT: D 740 THR cc_start: 0.7947 (m) cc_final: 0.7657 (p) outliers start: 47 outliers final: 19 residues processed: 339 average time/residue: 1.6438 time to fit residues: 625.0954 Evaluate side-chains 323 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN B 279 GLN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN D 279 GLN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22222 Z= 0.225 Angle : 0.572 11.045 29822 Z= 0.278 Chirality : 0.038 0.147 3233 Planarity : 0.003 0.030 3600 Dihedral : 16.286 115.933 3885 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.98 % Allowed : 15.39 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.16), residues: 2484 helix: 1.13 (0.12), residues: 1632 sheet: 2.42 (0.60), residues: 64 loop : -1.36 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 710 HIS 0.007 0.001 HIS A 301 PHE 0.014 0.001 PHE B 506 TYR 0.015 0.002 TYR B 208 ARG 0.002 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 298 time to evaluate : 2.428 Fit side-chains REVERT: A 185 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6821 (mm-30) REVERT: A 253 LYS cc_start: 0.7148 (mppt) cc_final: 0.6904 (mppt) REVERT: A 280 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (tp) REVERT: A 370 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7633 (pp) REVERT: A 447 PHE cc_start: 0.8602 (m-80) cc_final: 0.8386 (m-10) REVERT: A 485 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6262 (tp) REVERT: A 488 MET cc_start: 0.6641 (mmt) cc_final: 0.6308 (mtm) REVERT: A 500 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7428 (ttpt) REVERT: A 562 MET cc_start: 0.9212 (mmt) cc_final: 0.8720 (mmt) REVERT: A 619 CYS cc_start: 0.6134 (p) cc_final: 0.5896 (p) REVERT: A 687 GLU cc_start: 0.7776 (pt0) cc_final: 0.7402 (pp20) REVERT: A 729 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: A 738 LYS cc_start: 0.8113 (pttt) cc_final: 0.7819 (pttm) REVERT: A 740 THR cc_start: 0.8038 (m) cc_final: 0.7764 (p) REVERT: B 159 MET cc_start: 0.6964 (mmm) cc_final: 0.6250 (mmm) REVERT: B 185 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6925 (mm-30) REVERT: B 253 LYS cc_start: 0.7119 (mppt) cc_final: 0.6870 (mppt) REVERT: B 280 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8456 (tp) REVERT: B 485 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6284 (tp) REVERT: B 488 MET cc_start: 0.6566 (mmt) cc_final: 0.6287 (mtm) REVERT: B 514 GLN cc_start: 0.6947 (tt0) cc_final: 0.6407 (mm-40) REVERT: B 562 MET cc_start: 0.9213 (mmt) cc_final: 0.8750 (mmt) REVERT: B 619 CYS cc_start: 0.6107 (p) cc_final: 0.5873 (p) REVERT: B 738 LYS cc_start: 0.8156 (pttt) cc_final: 0.7838 (ptpp) REVERT: B 740 THR cc_start: 0.7986 (m) cc_final: 0.7772 (p) REVERT: C 159 MET cc_start: 0.7077 (mmm) cc_final: 0.6257 (mmm) REVERT: C 185 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6909 (mm-30) REVERT: C 280 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8441 (tp) REVERT: C 283 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: C 351 MET cc_start: 0.9221 (mtp) cc_final: 0.9002 (mtp) REVERT: C 488 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6277 (mtm) REVERT: C 514 GLN cc_start: 0.7060 (tt0) cc_final: 0.6419 (mm-40) REVERT: C 562 MET cc_start: 0.9200 (mmt) cc_final: 0.8844 (mmt) REVERT: C 619 CYS cc_start: 0.6104 (p) cc_final: 0.5885 (p) REVERT: C 738 LYS cc_start: 0.8144 (pttt) cc_final: 0.7832 (ptpp) REVERT: C 740 THR cc_start: 0.7983 (m) cc_final: 0.7769 (p) REVERT: D 159 MET cc_start: 0.7168 (mmm) cc_final: 0.6156 (mmm) REVERT: D 185 GLU cc_start: 0.7278 (mm-30) cc_final: 0.7000 (mm-30) REVERT: D 280 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8464 (tp) REVERT: D 447 PHE cc_start: 0.8626 (m-80) cc_final: 0.8416 (m-10) REVERT: D 485 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6308 (tp) REVERT: D 488 MET cc_start: 0.6668 (mmt) cc_final: 0.6331 (mtm) REVERT: D 514 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6549 (mm-40) REVERT: D 562 MET cc_start: 0.9161 (mmt) cc_final: 0.8792 (mmt) REVERT: D 619 CYS cc_start: 0.6115 (p) cc_final: 0.5896 (p) REVERT: D 738 LYS cc_start: 0.8138 (pttt) cc_final: 0.7827 (ptpp) REVERT: D 740 THR cc_start: 0.7984 (m) cc_final: 0.7750 (p) outliers start: 66 outliers final: 28 residues processed: 345 average time/residue: 1.5339 time to fit residues: 590.6358 Evaluate side-chains 336 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 295 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 514 GLN Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22222 Z= 0.184 Angle : 0.538 10.601 29822 Z= 0.263 Chirality : 0.037 0.147 3233 Planarity : 0.003 0.032 3600 Dihedral : 16.125 117.638 3885 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.17 % Allowed : 16.16 % Favored : 81.68 % 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: 0.64 (0.16), residues: 2484 helix: 1.21 (0.12), residues: 1624 sheet: 2.43 (0.58), residues: 64 loop : -1.38 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 710 HIS 0.006 0.001 HIS C 301 PHE 0.015 0.001 PHE D 506 TYR 0.015 0.002 TYR A 208 ARG 0.003 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 305 time to evaluate : 2.666 Fit side-chains REVERT: A 185 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 253 LYS cc_start: 0.7080 (mppt) cc_final: 0.6845 (mppt) REVERT: A 280 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 370 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 447 PHE cc_start: 0.8597 (m-80) cc_final: 0.8375 (m-10) REVERT: A 485 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6268 (tp) REVERT: A 488 MET cc_start: 0.6547 (mmt) cc_final: 0.6282 (mtm) REVERT: A 562 MET cc_start: 0.9189 (mmt) cc_final: 0.8708 (mmt) REVERT: A 619 CYS cc_start: 0.6113 (p) cc_final: 0.5878 (p) REVERT: A 687 GLU cc_start: 0.7765 (pt0) cc_final: 0.7393 (pp20) REVERT: A 729 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7820 (mtp180) REVERT: A 738 LYS cc_start: 0.8097 (pttt) cc_final: 0.7826 (pttm) REVERT: A 740 THR cc_start: 0.8003 (m) cc_final: 0.7695 (p) REVERT: B 159 MET cc_start: 0.6917 (mmm) cc_final: 0.6384 (mmm) REVERT: B 185 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6801 (mm-30) REVERT: B 253 LYS cc_start: 0.7071 (mppt) cc_final: 0.6836 (mppt) REVERT: B 280 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 369 ARG cc_start: 0.7068 (tmm160) cc_final: 0.6821 (tmm160) REVERT: B 485 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6286 (tp) REVERT: B 488 MET cc_start: 0.6543 (mmt) cc_final: 0.6266 (mtm) REVERT: B 514 GLN cc_start: 0.6944 (tt0) cc_final: 0.6404 (mm-40) REVERT: B 562 MET cc_start: 0.9205 (mmt) cc_final: 0.8748 (mmt) REVERT: B 619 CYS cc_start: 0.6090 (p) cc_final: 0.5855 (p) REVERT: B 738 LYS cc_start: 0.8111 (pttt) cc_final: 0.7798 (ptpp) REVERT: B 740 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7656 (p) REVERT: C 159 MET cc_start: 0.7089 (mmm) cc_final: 0.6173 (mmm) REVERT: C 185 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6813 (mm-30) REVERT: C 351 MET cc_start: 0.9222 (mtp) cc_final: 0.9016 (mtp) REVERT: C 369 ARG cc_start: 0.7072 (tmm160) cc_final: 0.6824 (tmm160) REVERT: C 488 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6266 (mtm) REVERT: C 514 GLN cc_start: 0.7068 (tt0) cc_final: 0.6438 (mm-40) REVERT: C 562 MET cc_start: 0.9202 (mmt) cc_final: 0.8723 (mmt) REVERT: C 619 CYS cc_start: 0.6085 (p) cc_final: 0.5868 (p) REVERT: C 738 LYS cc_start: 0.8109 (pttt) cc_final: 0.7798 (ptpp) REVERT: C 740 THR cc_start: 0.7930 (m) cc_final: 0.7651 (p) REVERT: D 159 MET cc_start: 0.7203 (mmm) cc_final: 0.6242 (mmm) REVERT: D 185 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6789 (mm-30) REVERT: D 280 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8443 (tp) REVERT: D 369 ARG cc_start: 0.7074 (tmm160) cc_final: 0.6824 (tmm160) REVERT: D 447 PHE cc_start: 0.8630 (m-80) cc_final: 0.8418 (m-10) REVERT: D 488 MET cc_start: 0.6573 (mmt) cc_final: 0.6308 (mtm) REVERT: D 514 GLN cc_start: 0.7092 (tt0) cc_final: 0.6540 (mm-40) REVERT: D 562 MET cc_start: 0.9162 (mmt) cc_final: 0.8662 (mmt) REVERT: D 619 CYS cc_start: 0.6094 (p) cc_final: 0.5873 (p) REVERT: D 687 GLU cc_start: 0.7832 (pt0) cc_final: 0.7532 (pt0) REVERT: D 738 LYS cc_start: 0.8107 (pttt) cc_final: 0.7794 (ptpp) REVERT: D 740 THR cc_start: 0.7931 (m) cc_final: 0.7646 (p) outliers start: 48 outliers final: 28 residues processed: 343 average time/residue: 1.5552 time to fit residues: 594.7040 Evaluate side-chains 340 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 548 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN ** C 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN ** D 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22222 Z= 0.196 Angle : 0.552 10.741 29822 Z= 0.270 Chirality : 0.038 0.151 3233 Planarity : 0.003 0.031 3600 Dihedral : 16.101 116.756 3885 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.21 % Allowed : 16.43 % Favored : 81.36 % 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: 0.62 (0.16), residues: 2484 helix: 1.18 (0.12), residues: 1632 sheet: 2.42 (0.59), residues: 64 loop : -1.40 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 710 HIS 0.006 0.001 HIS D 301 PHE 0.017 0.001 PHE D 506 TYR 0.020 0.002 TYR C 208 ARG 0.003 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4968 Ramachandran restraints generated. 2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 305 time to evaluate : 2.357 Fit side-chains REVERT: A 185 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6907 (mm-30) REVERT: A 253 LYS cc_start: 0.7195 (mppt) cc_final: 0.6847 (mppt) REVERT: A 370 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7670 (pp) REVERT: A 447 PHE cc_start: 0.8596 (m-80) cc_final: 0.8382 (m-10) REVERT: A 485 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6273 (tp) REVERT: A 488 MET cc_start: 0.6549 (mmt) cc_final: 0.6282 (mtm) REVERT: A 562 MET cc_start: 0.9190 (mmt) cc_final: 0.8709 (mmt) REVERT: A 619 CYS cc_start: 0.6112 (p) cc_final: 0.5876 (p) REVERT: A 687 GLU cc_start: 0.7773 (pt0) cc_final: 0.7395 (pp20) REVERT: A 729 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: A 738 LYS cc_start: 0.8099 (pttt) cc_final: 0.7833 (pttm) REVERT: A 740 THR cc_start: 0.8007 (m) cc_final: 0.7723 (p) REVERT: B 159 MET cc_start: 0.6924 (mmm) cc_final: 0.6104 (mmm) REVERT: B 185 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6814 (mm-30) REVERT: B 253 LYS cc_start: 0.7188 (mppt) cc_final: 0.6840 (mppt) REVERT: B 280 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 369 ARG cc_start: 0.7070 (tmm160) cc_final: 0.6846 (tmm160) REVERT: B 370 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7637 (pp) REVERT: B 485 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6287 (tp) REVERT: B 488 MET cc_start: 0.6549 (mmt) cc_final: 0.6265 (mtm) REVERT: B 514 GLN cc_start: 0.6924 (tt0) cc_final: 0.6398 (mm-40) REVERT: B 562 MET cc_start: 0.9207 (mmt) cc_final: 0.8755 (mmt) REVERT: B 619 CYS cc_start: 0.6095 (p) cc_final: 0.5860 (p) REVERT: B 738 LYS cc_start: 0.8132 (pttt) cc_final: 0.7818 (ptpp) REVERT: B 740 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7674 (p) REVERT: C 159 MET cc_start: 0.7090 (mmm) cc_final: 0.6176 (mmm) REVERT: C 185 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6859 (mm-30) REVERT: C 280 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8427 (tp) REVERT: C 351 MET cc_start: 0.9223 (mtp) cc_final: 0.9017 (mtp) REVERT: C 369 ARG cc_start: 0.7071 (tmm160) cc_final: 0.6846 (tmm160) REVERT: C 370 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7640 (pp) REVERT: C 488 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6257 (mtm) REVERT: C 514 GLN cc_start: 0.6969 (tt0) cc_final: 0.6383 (mm-40) REVERT: C 562 MET cc_start: 0.9196 (mmt) cc_final: 0.8712 (mmt) REVERT: C 619 CYS cc_start: 0.6082 (p) cc_final: 0.5865 (p) REVERT: C 738 LYS cc_start: 0.8122 (pttt) cc_final: 0.7812 (ptpp) REVERT: C 740 THR cc_start: 0.7912 (m) cc_final: 0.7646 (p) REVERT: D 159 MET cc_start: 0.7168 (mmm) cc_final: 0.6185 (mmm) REVERT: D 185 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6874 (mm-30) REVERT: D 280 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8441 (tp) REVERT: D 369 ARG cc_start: 0.7072 (tmm160) cc_final: 0.6844 (tmm160) REVERT: D 370 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7643 (pp) REVERT: D 447 PHE cc_start: 0.8629 (m-80) cc_final: 0.8419 (m-10) REVERT: D 485 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6309 (tp) REVERT: D 488 MET cc_start: 0.6577 (mmt) cc_final: 0.6307 (mtm) REVERT: D 514 GLN cc_start: 0.7095 (tt0) cc_final: 0.6546 (mm-40) REVERT: D 562 MET cc_start: 0.9159 (mmt) cc_final: 0.8659 (mmt) REVERT: D 619 CYS cc_start: 0.6100 (p) cc_final: 0.5880 (p) REVERT: D 687 GLU cc_start: 0.7852 (pt0) cc_final: 0.7549 (pt0) REVERT: D 738 LYS cc_start: 0.8120 (pttt) cc_final: 0.7810 (ptpp) REVERT: D 740 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7640 (p) outliers start: 49 outliers final: 31 residues processed: 344 average time/residue: 1.5756 time to fit residues: 604.5944 Evaluate side-chains 349 residues out of total 2216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 304 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 743 LYS Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 418 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 743 LYS Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 740 THR Chi-restraints excluded: chain D residue 743 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN A 750 ASN ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS B 750 ASN C 452 ASN C 750 ASN D 160 HIS D 452 ASN D 750 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.160395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126231 restraints weight = 23053.384| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.66 r_work: 0.3288 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22222 Z= 0.154 Angle : 0.515 10.238 29822 Z= 0.253 Chirality : 0.036 0.149 3233 Planarity : 0.003 0.034 3600 Dihedral : 15.850 117.844 3885 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.76 % Allowed : 16.92 % Favored : 81.32 % 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: 0.75 (0.16), residues: 2484 helix: 1.32 (0.12), residues: 1624 sheet: 2.51 (0.58), residues: 64 loop : -1.41 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 710 HIS 0.008 0.001 HIS D 160 PHE 0.017 0.001 PHE C 506 TYR 0.019 0.001 TYR C 208 ARG 0.004 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9444.07 seconds wall clock time: 166 minutes 55.45 seconds (10015.45 seconds total)