Starting phenix.real_space_refine (version: dev) on Fri Apr 8 15:30:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmz_23443/04_2022/7lmz_23443_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B ASP 598": "OD1" <-> "OD2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C ASP 373": "OD1" <-> "OD2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E ASP 392": "OD1" <-> "OD2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E GLU 417": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E ASP 669": "OD1" <-> "OD2" Residue "E GLU 689": "OE1" <-> "OE2" Residue "E ASP 734": "OD1" <-> "OD2" Residue "F ASP 79": "OD1" <-> "OD2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F GLU 491": "OE1" <-> "OE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 598": "OD1" <-> "OD2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 34994 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 36, 'TRANS': 691, 'PCIS': 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 38, 'TRANS': 701, 'PCIS': 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 37, 'TRANS': 710, 'PCIS': 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 38, 'TRANS': 710, 'PCIS': 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 36, 'TRANS': 702, 'PCIS': 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 38, 'TRANS': 661, 'PCIS': 3} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 19.27, per 1000 atoms: 0.55 Number of scatterers: 34994 At special positions: 0 Unit cell: (163.702, 171.143, 135.001, 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 178 16.00 P 32 15.00 Mg 8 11.99 O 6656 8.00 N 6212 7.00 C 21908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.01 Conformation dependent library (CDL) restraints added in 5.4 seconds 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 213 helices and 37 sheets defined 43.7% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.000A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.594A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.226A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 592 through 611 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.562A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 274 No H-bonds generated for 'chain 'B' and resid 271 through 274' Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 332 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 547 removed outlier: 4.518A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 547' Processing helix chain 'B' and resid 554 through 568 Processing helix chain 'B' and resid 579 through 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 596 through 608 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 713 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 749 through 766 Processing helix chain 'C' and resid 13 through 16 removed outlier: 4.484A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 13 through 16' Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.157A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 332 removed outlier: 5.680A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 386 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 547 removed outlier: 4.150A pdb=" N LEU C 547 " --> pdb=" O GLY C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 547' Processing helix chain 'C' and resid 554 through 568 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 596 through 608 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.693A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 Processing helix chain 'D' and resid 13 through 16 removed outlier: 4.359A pdb=" N ILE D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 13 through 16' Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 274 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.530A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 409 through 426 removed outlier: 3.944A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 547 removed outlier: 3.817A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 544 through 547' Processing helix chain 'D' and resid 554 through 568 Processing helix chain 'D' and resid 579 through 582 No H-bonds generated for 'chain 'D' and resid 579 through 582' Processing helix chain 'D' and resid 592 through 608 removed outlier: 7.015A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 713 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 766 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 336 removed outlier: 4.331A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 No H-bonds generated for 'chain 'E' and resid 355 through 358' Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 426 removed outlier: 3.510A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 554 through 568 Processing helix chain 'E' and resid 579 through 581 No H-bonds generated for 'chain 'E' and resid 579 through 581' Processing helix chain 'E' and resid 588 through 591 No H-bonds generated for 'chain 'E' and resid 588 through 591' Processing helix chain 'E' and resid 596 through 610 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 No H-bonds generated for 'chain 'E' and resid 631 through 634' Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.808A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 765 Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 138 No H-bonds generated for 'chain 'F' and resid 135 through 138' Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 409 through 426 removed outlier: 4.001A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 613 removed outlier: 4.534A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 634 No H-bonds generated for 'chain 'F' and resid 631 through 634' Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.183A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 713 Processing helix chain 'F' and resid 733 through 742 Processing helix chain 'F' and resid 749 through 761 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 7.714A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.883A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 115 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 169 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARG A 113 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 181 " --> pdb=" O ILE A 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 150 through 154 removed outlier: 3.603A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 369 removed outlier: 8.420A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 6.633A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= G, first strand: chain 'B' and resid 66 through 70 Processing sheet with id= H, first strand: chain 'B' and resid 113 through 115 removed outlier: 6.161A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= J, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.825A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 241 through 244 removed outlier: 7.025A pdb=" N ARG B 365 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N TYR B 244 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 367 " --> pdb=" O TYR B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 268 through 270 removed outlier: 8.751A pdb=" N ILE B 269 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 302 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 641 through 644 removed outlier: 8.236A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.590A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.618A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS C 115 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.828A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.252A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.283A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= T, first strand: chain 'D' and resid 38 through 41 removed outlier: 7.061A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.855A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 144 through 146 removed outlier: 3.691A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.197A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 641 through 645 removed outlier: 8.250A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= Z, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.346A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.581A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP E 169 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 144 through 146 removed outlier: 4.219A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 151 through 154 Processing sheet with id= AD, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.805A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.127A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 27 through 30 Processing sheet with id= AG, first strand: chain 'F' and resid 38 through 41 removed outlier: 7.908A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.561A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 151 through 154 Processing sheet with id= AJ, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.872A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE F 267 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 642 through 645 removed outlier: 7.956A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE F 645 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR F 517 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1237 hydrogen bonds defined for protein. 3609 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: 13.25 Time building geometry restraints manager: 15.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11941 1.34 - 1.46: 5692 1.46 - 1.58: 17620 1.58 - 1.70: 39 1.70 - 1.82: 284 Bond restraints: 35576 Sorted by residual: bond pdb=" CB PRO A 246 " pdb=" CG PRO A 246 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO B 372 " pdb=" CG PRO B 372 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO B 729 " pdb=" CG PRO B 729 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.64e+00 bond pdb=" N ASP E 169 " pdb=" CA ASP E 169 " ideal model delta sigma weight residual 1.462 1.445 0.017 1.05e-02 9.07e+03 2.52e+00 bond pdb=" CG PRO B 729 " pdb=" CD PRO B 729 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.28e+00 ... (remaining 35571 not shown) Histogram of bond angle deviations from ideal: 95.59 - 104.43: 730 104.43 - 113.27: 19967 113.27 - 122.11: 21371 122.11 - 130.95: 5925 130.95 - 139.79: 109 Bond angle restraints: 48102 Sorted by residual: angle pdb=" CA PRO A 246 " pdb=" N PRO A 246 " pdb=" CD PRO A 246 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.28e+01 angle pdb=" CA PRO B 729 " pdb=" N PRO B 729 " pdb=" CD PRO B 729 " ideal model delta sigma weight residual 112.00 104.50 7.50 1.40e+00 5.10e-01 2.87e+01 angle pdb=" CA PRO B 372 " pdb=" N PRO B 372 " pdb=" CD PRO B 372 " ideal model delta sigma weight residual 112.00 104.85 7.15 1.40e+00 5.10e-01 2.61e+01 angle pdb=" C VAL C 320 " pdb=" N GLU C 321 " pdb=" CA GLU C 321 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" N PRO B 729 " pdb=" CD PRO B 729 " pdb=" CG PRO B 729 " ideal model delta sigma weight residual 103.20 97.17 6.03 1.50e+00 4.44e-01 1.61e+01 ... (remaining 48097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 21492 31.57 - 63.14: 424 63.14 - 94.71: 41 94.71 - 126.28: 3 126.28 - 157.85: 5 Dihedral angle restraints: 21965 sinusoidal: 9193 harmonic: 12772 Sorted by residual: dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 97.85 -157.85 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 92.11 -152.11 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 74.49 -134.49 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 21962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3968 0.043 - 0.085: 980 0.085 - 0.128: 421 0.128 - 0.170: 34 0.170 - 0.213: 2 Chirality restraints: 5405 Sorted by residual: chirality pdb=" CB ILE F 707 " pdb=" CA ILE F 707 " pdb=" CG1 ILE F 707 " pdb=" CG2 ILE F 707 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL C 407 " pdb=" CA VAL C 407 " pdb=" CG1 VAL C 407 " pdb=" CG2 VAL C 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA GLU F 704 " pdb=" N GLU F 704 " pdb=" C GLU F 704 " pdb=" CB GLU F 704 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 5402 not shown) Planarity restraints: 6299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 245 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 246 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 728 " -0.065 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO B 729 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 371 " 0.056 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO B 372 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " 0.045 5.00e-02 4.00e+02 ... (remaining 6296 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 275 2.56 - 3.15: 28757 3.15 - 3.73: 57748 3.73 - 4.32: 80781 4.32 - 4.90: 130035 Nonbonded interactions: 297596 Sorted by model distance: nonbonded pdb=" O1G ATP C 902 " pdb="MG MG C 904 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 1.988 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 903 " model vdw 1.997 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 904 " model vdw 2.008 2.170 ... (remaining 297591 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 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 5 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'B' and (resid 23 through 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 178 5.16 5 C 21908 2.51 5 N 6212 2.21 5 O 6656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 10.210 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 88.050 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.004 0.111 35576 Z= 0.260 Angle : 0.652 11.620 48102 Z= 0.355 Chirality : 0.044 0.213 5405 Planarity : 0.006 0.120 6299 Dihedral : 13.048 157.850 13675 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.04 (0.12), residues: 4391 helix: 1.09 (0.12), residues: 1914 sheet: 0.76 (0.20), residues: 624 loop : 0.42 (0.14), residues: 1853 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.5879 time to fit residues: 251.5794 Evaluate side-chains 159 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 4.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.3980 chunk 334 optimal weight: 0.0070 chunk 185 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 chunk 225 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 345 optimal weight: 0.0570 chunk 133 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 400 optimal weight: 0.0770 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN F 578 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 35576 Z= 0.158 Angle : 0.546 9.891 48102 Z= 0.272 Chirality : 0.042 0.221 5405 Planarity : 0.005 0.085 6299 Dihedral : 7.367 161.678 4888 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.41 % Favored : 98.52 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.31 (0.13), residues: 4391 helix: 1.37 (0.12), residues: 1947 sheet: 0.78 (0.21), residues: 634 loop : 0.51 (0.15), residues: 1810 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 181 average time/residue: 0.4957 time to fit residues: 147.7798 Evaluate side-chains 145 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3122 time to fit residues: 6.6161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 110 optimal weight: 0.0020 chunk 401 optimal weight: 10.0000 chunk 433 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 chunk 397 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 321 optimal weight: 0.8980 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 35576 Z= 0.301 Angle : 0.562 8.052 48102 Z= 0.280 Chirality : 0.043 0.159 5405 Planarity : 0.005 0.084 6299 Dihedral : 7.307 173.375 4888 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.43 (0.13), residues: 4391 helix: 1.47 (0.12), residues: 1952 sheet: 0.71 (0.21), residues: 635 loop : 0.64 (0.15), residues: 1804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 176 average time/residue: 0.4968 time to fit residues: 146.8237 Evaluate side-chains 158 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 4.571 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3374 time to fit residues: 11.4817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 9.9990 chunk 301 optimal weight: 20.0000 chunk 208 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 402 optimal weight: 9.9990 chunk 426 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 381 optimal weight: 50.0000 chunk 114 optimal weight: 0.0030 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 35576 Z= 0.194 Angle : 0.514 9.646 48102 Z= 0.253 Chirality : 0.042 0.215 5405 Planarity : 0.004 0.076 6299 Dihedral : 7.155 179.151 4888 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.69 % Favored : 98.25 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.49 (0.13), residues: 4391 helix: 1.59 (0.12), residues: 1940 sheet: 0.69 (0.21), residues: 638 loop : 0.61 (0.15), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 173 average time/residue: 0.4706 time to fit residues: 137.7963 Evaluate side-chains 154 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3430 time to fit residues: 11.7988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 10.0000 chunk 241 optimal weight: 0.0570 chunk 6 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 175 optimal weight: 0.0040 chunk 363 optimal weight: 3.9990 chunk 294 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 217 optimal weight: 8.9990 chunk 382 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 overall best weight: 1.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 384 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 35576 Z= 0.198 Angle : 0.514 11.549 48102 Z= 0.253 Chirality : 0.042 0.279 5405 Planarity : 0.004 0.082 6299 Dihedral : 7.021 175.223 4888 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.89 % Favored : 98.06 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.51 (0.13), residues: 4391 helix: 1.62 (0.12), residues: 1945 sheet: 0.58 (0.20), residues: 652 loop : 0.65 (0.15), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 166 average time/residue: 0.4809 time to fit residues: 135.5883 Evaluate side-chains 155 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 4.539 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3503 time to fit residues: 11.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 84 optimal weight: 0.2980 chunk 250 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 426 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 224 optimal weight: 0.2980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN F 384 HIS F 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 35576 Z= 0.251 Angle : 0.526 10.843 48102 Z= 0.258 Chirality : 0.043 0.284 5405 Planarity : 0.004 0.069 6299 Dihedral : 6.942 171.061 4888 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.50 (0.13), residues: 4391 helix: 1.63 (0.12), residues: 1951 sheet: 0.55 (0.20), residues: 672 loop : 0.63 (0.15), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 165 average time/residue: 0.4462 time to fit residues: 126.7474 Evaluate side-chains 149 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 4.265 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3373 time to fit residues: 11.2834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 241 optimal weight: 0.0470 chunk 359 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 425 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 35576 Z= 0.180 Angle : 0.513 11.440 48102 Z= 0.249 Chirality : 0.042 0.295 5405 Planarity : 0.004 0.067 6299 Dihedral : 6.817 174.242 4888 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 98.00 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.57 (0.13), residues: 4391 helix: 1.70 (0.12), residues: 1935 sheet: 0.60 (0.20), residues: 652 loop : 0.66 (0.15), residues: 1804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 159 average time/residue: 0.4760 time to fit residues: 128.5387 Evaluate side-chains 146 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 4.214 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3353 time to fit residues: 8.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 270 optimal weight: 0.1980 chunk 289 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.312 35576 Z= 0.183 Angle : 0.528 17.374 48102 Z= 0.261 Chirality : 0.042 0.311 5405 Planarity : 0.004 0.095 6299 Dihedral : 6.692 175.149 4888 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.93 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.56 (0.13), residues: 4391 helix: 1.68 (0.12), residues: 1954 sheet: 0.64 (0.20), residues: 657 loop : 0.62 (0.15), residues: 1780 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 165 average time/residue: 0.4692 time to fit residues: 131.8603 Evaluate side-chains 151 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 4.500 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5156 time to fit residues: 9.1327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 0.8980 chunk 407 optimal weight: 1.9990 chunk 371 optimal weight: 50.0000 chunk 396 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 357 optimal weight: 4.9990 chunk 374 optimal weight: 50.0000 chunk 394 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 35576 Z= 0.273 Angle : 0.558 12.881 48102 Z= 0.273 Chirality : 0.043 0.289 5405 Planarity : 0.004 0.081 6299 Dihedral : 6.701 173.129 4888 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.44 % Favored : 97.49 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.57 (0.13), residues: 4391 helix: 1.70 (0.12), residues: 1938 sheet: 0.60 (0.20), residues: 657 loop : 0.66 (0.15), residues: 1796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 153 average time/residue: 0.4709 time to fit residues: 123.6954 Evaluate side-chains 148 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 4.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3647 time to fit residues: 9.8454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 439 optimal weight: 9.9990 chunk 404 optimal weight: 5.9990 chunk 349 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 35576 Z= 0.179 Angle : 0.542 14.014 48102 Z= 0.263 Chirality : 0.042 0.314 5405 Planarity : 0.004 0.077 6299 Dihedral : 6.539 171.208 4888 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 98.00 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.57 (0.13), residues: 4391 helix: 1.72 (0.12), residues: 1934 sheet: 0.62 (0.20), residues: 677 loop : 0.63 (0.15), residues: 1780 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.4979 time to fit residues: 125.2470 Evaluate side-chains 143 residues out of total 3783 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 5.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.9980 chunk 372 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 350 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 359 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 64 optimal weight: 8.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.101208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067021 restraints weight = 116281.027| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.58 r_work: 0.3225 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work: 0.3193 rms_B_bonded: 4.28 restraints_weight: 0.1250 r_work: 0.3178 rms_B_bonded: 4.30 restraints_weight: 0.0625 r_work: 0.3162 rms_B_bonded: 4.36 restraints_weight: 0.0312 r_work: 0.3147 rms_B_bonded: 4.43 restraints_weight: 0.0156 r_work: 0.3131 rms_B_bonded: 4.52 restraints_weight: 0.0078 r_work: 0.3114 rms_B_bonded: 4.63 restraints_weight: 0.0039 r_work: 0.3097 rms_B_bonded: 4.76 restraints_weight: 0.0020 r_work: 0.3080 rms_B_bonded: 4.91 restraints_weight: 0.0010 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 35576 Z= 0.187 Angle : 0.539 13.354 48102 Z= 0.261 Chirality : 0.042 0.293 5405 Planarity : 0.004 0.072 6299 Dihedral : 6.389 167.080 4888 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.57 (0.13), residues: 4391 helix: 1.66 (0.12), residues: 1962 sheet: 0.68 (0.20), residues: 655 loop : 0.66 (0.15), residues: 1774 =============================================================================== Job complete usr+sys time: 5314.77 seconds wall clock time: 99 minutes 4.81 seconds (5944.81 seconds total)