Starting phenix.real_space_refine on Sat Mar 23 00:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln3_23447/03_2024/7ln3_23447_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21867 2.51 5 N 6194 2.21 5 O 6643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C ASP 392": "OD1" <-> "OD2" Residue "C ASP 395": "OD1" <-> "OD2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C GLU 607": "OE1" <-> "OE2" Residue "C ASP 640": "OD1" <-> "OD2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 686": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D ASP 734": "OD1" <-> "OD2" Residue "D TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E ASP 410": "OD1" <-> "OD2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E GLU 488": "OE1" <-> "OE2" Residue "E PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E ASP 564": "OD1" <-> "OD2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E ASP 627": "OD1" <-> "OD2" Residue "E GLU 650": "OE1" <-> "OE2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "E TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F GLU 433": "OE1" <-> "OE2" Residue "F ASP 434": "OD1" <-> "OD2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 706": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34920 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: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 691} 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: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5784 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 700} 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: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} 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: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} 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: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5712 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 692} 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: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5504 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 659} Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.16, per 1000 atoms: 0.52 Number of scatterers: 34920 At special positions: 0 Unit cell: (165.148, 170.545, 138.163, 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 31 15.00 Mg 7 11.99 O 6643 8.00 N 6194 7.00 C 21867 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: 12.38 Conformation dependent library (CDL) restraints added in 6.5 seconds 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 39 sheets defined 43.1% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.87 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 199 Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.907A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 removed outlier: 4.124A 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 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 4.005A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.823A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 4.312A 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 661 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 713 removed outlier: 3.687A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) 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 91 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: 4.185A 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 358 Processing helix chain 'B' and resid 374 through 387 removed outlier: 4.264A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) 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 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: 4.374A 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 593 through 608 removed outlier: 6.354A pdb=" N ALA B 597 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 608 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 650 through 661 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 741 Processing helix chain 'B' and resid 749 through 766 Processing helix chain 'C' and resid 13 through 15 No H-bonds generated for 'chain 'C' and resid 13 through 15' Processing helix chain 'C' and resid 43 through 48 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 199 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: 4.231A 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 282 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 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' 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 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' 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 533 Processing helix chain 'C' and resid 544 through 547 removed outlier: 4.182A 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 650 through 661 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 Processing helix chain 'C' and resid 749 through 766 Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 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 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.018A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 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 295 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: 3.959A 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 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 546 No H-bonds generated for 'chain 'D' and resid 544 through 546' 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: 7.255A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.549A 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 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 No H-bonds generated for '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 337 removed outlier: 3.859A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.618A pdb=" N LYS E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 427 removed outlier: 3.582A 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 545 through 547 No H-bonds generated for 'chain 'E' and resid 545 through 547' Processing helix chain 'E' and resid 554 through 569 removed outlier: 3.765A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) 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 741 Processing helix chain 'E' and resid 749 through 765 Processing helix chain 'F' and resid 43 through 49 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 191 through 199 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 295 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 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 374 through 387 removed outlier: 3.990A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 409 through 425 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 506 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 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 661 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 99 through 101 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.345A pdb=" N VAL A 39 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE A 70 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 41 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 72 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 181 through 183 removed outlier: 3.865A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 113 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 169 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 115 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.697A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 365 through 368 removed outlier: 6.944A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 641 through 644 removed outlier: 6.780A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 27 through 30 Processing sheet with id= H, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.627A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 67 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.518A pdb=" N GLU B 167 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B 113 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= K, first strand: chain 'B' and resid 150 through 154 removed outlier: 4.014A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.617A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 641 through 645 removed outlier: 8.625A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 27 through 30 Processing sheet with id= O, first strand: chain 'C' and resid 38 through 42 removed outlier: 8.073A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.613A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.671A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.533A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 641 through 645 removed outlier: 8.404A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= U, first strand: chain 'D' and resid 38 through 41 removed outlier: 7.518A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.504A pdb=" N ARG D 113 " --> pdb=" O ASP D 169 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL D 181 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.372A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.300A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 641 through 645 removed outlier: 8.458A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.624A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 109 through 111 Processing sheet with id= AB, first strand: chain 'E' and resid 113 through 115 removed outlier: 4.230A pdb=" N ARG E 113 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP E 169 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS E 115 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.593A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.851A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.613A 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: 8.351A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= AG, first strand: chain 'F' and resid 39 through 42 Processing sheet with id= AH, first strand: chain 'F' and resid 67 through 70 removed outlier: 3.526A pdb=" N ALA F 67 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.920A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AK, first strand: chain 'F' and resid 150 through 154 Processing sheet with id= AL, first strand: chain 'F' and resid 365 through 368 removed outlier: 5.884A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.866A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3648 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: 13.70 Time building geometry restraints manager: 13.47 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: 11907 1.34 - 1.46: 5916 1.46 - 1.58: 17370 1.58 - 1.70: 26 1.70 - 1.82: 284 Bond restraints: 35503 Sorted by residual: bond pdb=" CB PRO A 238 " pdb=" CG PRO A 238 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.21e+00 bond pdb=" N THR A 549 " pdb=" CA THR A 549 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.38e+00 bond pdb=" CB MET E 84 " pdb=" CG MET E 84 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.37e+00 bond pdb=" CA ALA A 297 " pdb=" C ALA A 297 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.26e-02 6.30e+03 2.22e+00 bond pdb=" CB PRO F 727 " pdb=" CG PRO F 727 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.88e+00 ... (remaining 35498 not shown) Histogram of bond angle deviations from ideal: 96.52 - 105.13: 874 105.13 - 113.74: 20412 113.74 - 122.35: 22031 122.35 - 130.96: 4578 130.96 - 139.57: 110 Bond angle restraints: 48005 Sorted by residual: angle pdb=" CB MET E 84 " pdb=" CG MET E 84 " pdb=" SD MET E 84 " ideal model delta sigma weight residual 112.70 96.64 16.06 3.00e+00 1.11e-01 2.86e+01 angle pdb=" CA PRO A 298 " pdb=" N PRO A 298 " pdb=" CD PRO A 298 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CA PRO A 238 " pdb=" N PRO A 238 " pdb=" CD PRO A 238 " ideal model delta sigma weight residual 112.00 106.24 5.76 1.40e+00 5.10e-01 1.69e+01 angle pdb=" C LYS F 336 " pdb=" N GLN F 337 " pdb=" CA GLN F 337 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 118.44 124.56 -6.12 1.59e+00 3.96e-01 1.48e+01 ... (remaining 48000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 21498 31.74 - 63.48: 568 63.48 - 95.21: 65 95.21 - 126.95: 4 126.95 - 158.69: 4 Dihedral angle restraints: 22139 sinusoidal: 9376 harmonic: 12763 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 98.69 -158.69 1 2.00e+01 2.50e-03 4.64e+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 77.77 -137.77 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O2A ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PA ADP F 902 " pdb=" PB ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.72 -132.72 1 2.00e+01 2.50e-03 4.03e+01 ... (remaining 22136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3611 0.037 - 0.074: 1184 0.074 - 0.110: 476 0.110 - 0.147: 123 0.147 - 0.184: 3 Chirality restraints: 5397 Sorted by residual: chirality pdb=" CB ILE E 82 " pdb=" CA ILE E 82 " pdb=" CG1 ILE E 82 " pdb=" CG2 ILE E 82 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA GLU D 261 " pdb=" N GLU D 261 " pdb=" C GLU D 261 " pdb=" CB GLU D 261 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB THR C 467 " pdb=" CA THR C 467 " pdb=" OG1 THR C 467 " pdb=" CG2 THR C 467 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 5394 not shown) Planarity restraints: 6286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 237 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A 238 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 635 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO F 636 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO F 636 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 636 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 171 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO F 172 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 172 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 172 " -0.034 5.00e-02 4.00e+02 ... (remaining 6283 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 205 2.54 - 3.13: 27361 3.13 - 3.72: 55709 3.72 - 4.31: 77288 4.31 - 4.90: 126791 Nonbonded interactions: 287354 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 1.950 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 2.039 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.043 2.170 nonbonded pdb=" O1B ATP E 902 " pdb="MG MG E 904 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 2.057 2.170 ... (remaining 287349 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 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 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 'B' and (resid 23 through 406 or (resid 407 and (name N or name CA or nam \ e C or name O or name CB )) or resid 408 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 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 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) 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 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) 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 406 or (resid 407 and (name N o \ r name CA or name C or name O or name CB )) or resid 408 through 461 or resid 47 \ 2 through 507 or (resid 508 and (name N or name CA or name C or name O or name C \ B )) or resid 509 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) 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 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 533 or (resid 5 \ 34 and (name N or name CA or name C or name O or name CB )) or resid 535 through \ 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.860 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 90.740 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 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 : 0.005 0.103 35503 Z= 0.309 Angle : 0.674 16.056 48005 Z= 0.359 Chirality : 0.044 0.184 5397 Planarity : 0.005 0.091 6286 Dihedral : 14.414 158.690 13855 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.48 (0.12), residues: 4375 helix: 1.52 (0.12), residues: 1936 sheet: 1.30 (0.21), residues: 590 loop : 0.42 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 454 HIS 0.006 0.001 HIS F 406 PHE 0.022 0.002 PHE A 768 TYR 0.018 0.002 TYR C 644 ARG 0.007 0.001 ARG F 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 508 MET cc_start: 0.7861 (mmm) cc_final: 0.7501 (mmm) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.5500 time to fit residues: 213.7468 Evaluate side-chains 152 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 178 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 401 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 327 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 384 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN F 578 GLN F 603 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35503 Z= 0.289 Angle : 0.599 10.096 48005 Z= 0.298 Chirality : 0.042 0.169 5397 Planarity : 0.005 0.092 6286 Dihedral : 10.299 162.911 5107 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.55 % Favored : 98.38 % Rotamer: Outliers : 0.48 % Allowed : 5.46 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.71 (0.13), residues: 4375 helix: 1.86 (0.12), residues: 1920 sheet: 0.95 (0.20), residues: 632 loop : 0.56 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.006 0.001 HIS F 406 PHE 0.018 0.001 PHE C 52 TYR 0.011 0.001 TYR C 173 ARG 0.011 0.001 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 3.720 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: C 508 MET cc_start: 0.7781 (mmm) cc_final: 0.7375 (mmm) REVERT: E 46 MET cc_start: -0.0132 (ptp) cc_final: -0.1168 (ttm) outliers start: 18 outliers final: 5 residues processed: 177 average time/residue: 0.4920 time to fit residues: 142.4575 Evaluate side-chains 155 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain E residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 0.1980 chunk 273 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 402 optimal weight: 9.9990 chunk 434 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 chunk 398 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 322 optimal weight: 0.0770 overall best weight: 3.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 533 ASN C 603 GLN D 103 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35503 Z= 0.298 Angle : 0.576 9.464 48005 Z= 0.286 Chirality : 0.042 0.156 5397 Planarity : 0.004 0.062 6286 Dihedral : 9.874 173.926 5107 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Rotamer: Outliers : 0.83 % Allowed : 6.92 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.79 (0.13), residues: 4375 helix: 1.93 (0.12), residues: 1937 sheet: 0.97 (0.20), residues: 606 loop : 0.59 (0.15), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 551 HIS 0.006 0.001 HIS F 406 PHE 0.021 0.001 PHE F 363 TYR 0.016 0.001 TYR B 134 ARG 0.008 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 3.846 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: C 508 MET cc_start: 0.7745 (mmm) cc_final: 0.7270 (mmm) REVERT: D 158 MET cc_start: 0.6466 (ppp) cc_final: 0.6018 (pmm) REVERT: E 46 MET cc_start: 0.0137 (ptp) cc_final: -0.0070 (ptp) outliers start: 31 outliers final: 9 residues processed: 178 average time/residue: 0.4482 time to fit residues: 132.3828 Evaluate side-chains 147 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 403 optimal weight: 9.9990 chunk 427 optimal weight: 9.9990 chunk 210 optimal weight: 0.0270 chunk 382 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35503 Z= 0.231 Angle : 0.548 9.493 48005 Z= 0.269 Chirality : 0.041 0.149 5397 Planarity : 0.004 0.066 6286 Dihedral : 9.461 174.571 5107 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 8.29 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.86 (0.13), residues: 4375 helix: 2.03 (0.12), residues: 1916 sheet: 0.96 (0.21), residues: 604 loop : 0.61 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 551 HIS 0.004 0.001 HIS F 406 PHE 0.016 0.001 PHE A 302 TYR 0.013 0.001 TYR D 134 ARG 0.007 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 4.002 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: C 508 MET cc_start: 0.7735 (mmm) cc_final: 0.7200 (mmm) outliers start: 33 outliers final: 14 residues processed: 171 average time/residue: 0.4847 time to fit residues: 137.1541 Evaluate side-chains 153 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 4.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 218 optimal weight: 1.9990 chunk 383 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 HIS B 406 HIS ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 35503 Z= 0.392 Angle : 0.637 9.765 48005 Z= 0.314 Chirality : 0.042 0.166 5397 Planarity : 0.004 0.065 6286 Dihedral : 9.338 156.224 5107 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 9.77 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.69 (0.13), residues: 4375 helix: 1.86 (0.12), residues: 1930 sheet: 0.89 (0.21), residues: 611 loop : 0.53 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.006 0.001 HIS F 406 PHE 0.014 0.002 PHE A 302 TYR 0.014 0.001 TYR B 134 ARG 0.006 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 4.047 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: B 158 MET cc_start: 0.1215 (pmm) cc_final: 0.0950 (pmm) REVERT: C 508 MET cc_start: 0.7791 (mmm) cc_final: 0.7127 (mmm) outliers start: 45 outliers final: 27 residues processed: 179 average time/residue: 0.4483 time to fit residues: 135.3403 Evaluate side-chains 168 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 0.9990 chunk 384 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 427 optimal weight: 0.0570 chunk 355 optimal weight: 0.0570 chunk 198 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS D 103 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35503 Z= 0.142 Angle : 0.533 9.559 48005 Z= 0.260 Chirality : 0.041 0.197 5397 Planarity : 0.004 0.059 6286 Dihedral : 8.851 155.441 5107 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.35 % Favored : 98.58 % Rotamer: Outliers : 0.83 % Allowed : 10.95 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.91 (0.13), residues: 4375 helix: 2.08 (0.12), residues: 1917 sheet: 0.96 (0.21), residues: 597 loop : 0.64 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.021 0.001 HIS B 404 PHE 0.018 0.001 PHE E 363 TYR 0.007 0.001 TYR A 244 ARG 0.003 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 4.098 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: B 158 MET cc_start: 0.0881 (pmm) cc_final: 0.0676 (pmm) REVERT: C 508 MET cc_start: 0.7650 (mmm) cc_final: 0.7065 (mmm) outliers start: 31 outliers final: 18 residues processed: 169 average time/residue: 0.4854 time to fit residues: 138.7388 Evaluate side-chains 158 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 7.9990 chunk 48 optimal weight: 0.0870 chunk 243 optimal weight: 6.9990 chunk 312 optimal weight: 50.0000 chunk 241 optimal weight: 5.9990 chunk 359 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 426 optimal weight: 20.0000 chunk 266 optimal weight: 0.0770 chunk 259 optimal weight: 8.9990 chunk 196 optimal weight: 0.0030 overall best weight: 1.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35503 Z= 0.164 Angle : 0.527 9.820 48005 Z= 0.256 Chirality : 0.041 0.183 5397 Planarity : 0.004 0.056 6286 Dihedral : 8.596 150.484 5107 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.44 % Favored : 98.49 % Rotamer: Outliers : 0.73 % Allowed : 11.33 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.97 (0.13), residues: 4375 helix: 2.12 (0.12), residues: 1921 sheet: 1.02 (0.21), residues: 609 loop : 0.65 (0.15), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.024 0.001 HIS B 404 PHE 0.014 0.001 PHE F 363 TYR 0.021 0.001 TYR A 173 ARG 0.006 0.000 ARG C 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 3.819 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: C 508 MET cc_start: 0.7686 (mmm) cc_final: 0.7088 (mmm) outliers start: 27 outliers final: 23 residues processed: 164 average time/residue: 0.4652 time to fit residues: 128.6598 Evaluate side-chains 161 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 40.0000 chunk 270 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35503 Z= 0.248 Angle : 0.562 9.751 48005 Z= 0.275 Chirality : 0.041 0.161 5397 Planarity : 0.004 0.058 6286 Dihedral : 8.546 144.984 5107 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Rotamer: Outliers : 0.89 % Allowed : 11.33 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.13), residues: 4375 helix: 2.15 (0.12), residues: 1918 sheet: 1.07 (0.21), residues: 606 loop : 0.65 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.012 0.001 HIS B 404 PHE 0.011 0.001 PHE E 360 TYR 0.010 0.001 TYR A 173 ARG 0.016 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 4.012 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: A 275 MET cc_start: 0.1157 (OUTLIER) cc_final: 0.0605 (mtt) REVERT: C 508 MET cc_start: 0.7743 (mmm) cc_final: 0.7077 (mmm) REVERT: F 84 MET cc_start: 0.0144 (mmp) cc_final: -0.0717 (mpp) outliers start: 33 outliers final: 25 residues processed: 164 average time/residue: 0.4706 time to fit residues: 129.1556 Evaluate side-chains 163 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 20.0000 chunk 408 optimal weight: 20.0000 chunk 372 optimal weight: 40.0000 chunk 396 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 358 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35503 Z= 0.271 Angle : 0.577 10.310 48005 Z= 0.281 Chirality : 0.041 0.197 5397 Planarity : 0.004 0.058 6286 Dihedral : 8.518 137.939 5107 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer: Outliers : 0.81 % Allowed : 11.68 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.95 (0.13), residues: 4375 helix: 2.09 (0.12), residues: 1936 sheet: 0.99 (0.21), residues: 617 loop : 0.65 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 454 HIS 0.030 0.001 HIS B 404 PHE 0.039 0.001 PHE A 768 TYR 0.010 0.001 TYR B 134 ARG 0.006 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 4.278 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: A 275 MET cc_start: 0.1218 (OUTLIER) cc_final: 0.0663 (mtt) REVERT: C 508 MET cc_start: 0.7760 (mmm) cc_final: 0.7082 (mmm) REVERT: F 84 MET cc_start: 0.0076 (mmp) cc_final: -0.0866 (mpp) outliers start: 30 outliers final: 23 residues processed: 161 average time/residue: 0.4652 time to fit residues: 126.6369 Evaluate side-chains 160 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 0.8980 chunk 419 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 440 optimal weight: 10.0000 chunk 405 optimal weight: 3.9990 chunk 350 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 270 optimal weight: 0.0270 chunk 215 optimal weight: 7.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35503 Z= 0.176 Angle : 0.553 11.497 48005 Z= 0.268 Chirality : 0.041 0.173 5397 Planarity : 0.004 0.058 6286 Dihedral : 8.327 134.374 5107 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.51 % Favored : 98.42 % Rotamer: Outliers : 0.67 % Allowed : 11.89 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % 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: 1.98 (0.13), residues: 4375 helix: 2.12 (0.12), residues: 1922 sheet: 1.04 (0.21), residues: 617 loop : 0.68 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 454 HIS 0.020 0.001 HIS B 404 PHE 0.025 0.001 PHE A 768 TYR 0.007 0.001 TYR F 495 ARG 0.005 0.000 ARG C 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8750 Ramachandran restraints generated. 4375 Oldfield, 0 Emsley, 4375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 3.977 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: A 275 MET cc_start: 0.1154 (OUTLIER) cc_final: 0.0646 (mtt) REVERT: A 757 MET cc_start: 0.6274 (ppp) cc_final: 0.6013 (ppp) REVERT: C 508 MET cc_start: 0.7704 (mmm) cc_final: 0.7013 (mmm) outliers start: 25 outliers final: 20 residues processed: 158 average time/residue: 0.4644 time to fit residues: 124.2201 Evaluate side-chains 156 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 2.9990 chunk 373 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 323 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 351 optimal weight: 0.0980 chunk 146 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 44 optimal weight: 0.0570 chunk 64 optimal weight: 8.9990 overall best weight: 2.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.090795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059806 restraints weight = 173125.544| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.97 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35503 Z= 0.197 Angle : 0.569 15.808 48005 Z= 0.276 Chirality : 0.041 0.199 5397 Planarity : 0.004 0.056 6286 Dihedral : 8.229 127.434 5107 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.31 % Rotamer: Outliers : 0.70 % Allowed : 11.92 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.13), residues: 4375 helix: 2.13 (0.12), residues: 1924 sheet: 1.05 (0.21), residues: 617 loop : 0.69 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.004 0.001 HIS B 317 PHE 0.022 0.001 PHE A 768 TYR 0.010 0.001 TYR B 134 ARG 0.002 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5698.21 seconds wall clock time: 104 minutes 57.04 seconds (6297.04 seconds total)