Starting phenix.real_space_refine on Fri Mar 22 22:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ln1_23445/03_2024/7ln1_23445_updated.pdb" } resolution = 3.4 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 21790 2.51 5 N 6171 2.21 5 O 6619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 66": "OE1" <-> "OE2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 756": "OE1" <-> "OE2" Residue "B PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ASP 373": "OD1" <-> "OD2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 649": "OD1" <-> "OD2" Residue "C GLU 710": "OE1" <-> "OE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D GLU 738": "OE1" <-> "OE2" Residue "D PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 395": "OD1" <-> "OD2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 556": "OE1" <-> "OE2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E ASP 669": "OD1" <-> "OD2" Residue "E ASP 686": "OD1" <-> "OD2" Residue "E GLU 704": "OE1" <-> "OE2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 756": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ASP 304": "OD1" <-> "OD2" Residue "F ASP 373": "OD1" <-> "OD2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ASP 395": "OD1" <-> "OD2" Residue "F ASP 410": "OD1" <-> "OD2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "F GLU 488": "OE1" <-> "OE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F ASP 598": "OD1" <-> "OD2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F GLU 710": "OE1" <-> "OE2" Residue "F GLU 712": "OE1" <-> "OE2" Residue "F ASP 734": "OD1" <-> "OD2" Residue "F GLU 737": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34796 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': 4, 'PTRANS': 36, '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: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5698 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 690} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 5778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5778 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 700} 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: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 661} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 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: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 17.62, per 1000 atoms: 0.51 Number of scatterers: 34796 At special positions: 0 Unit cell: (162.639, 171.143, 136.064, 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 6619 8.00 N 6171 7.00 C 21790 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: 11.61 Conformation dependent library (CDL) restraints added in 5.5 seconds 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 37 sheets defined 43.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.70 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 139 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.084A 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 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.938A 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 613 removed outlier: 4.699A pdb=" N THR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) 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 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 86 through 92 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.631A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.082A 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 333 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: 4.975A 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 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.746A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) 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 554 through 568 Processing helix chain 'B' and resid 579 through 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 596 through 608 Processing helix chain 'B' and resid 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 742 Processing helix chain 'B' and resid 749 through 766 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 198 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.540A 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 271 through 274 No H-bonds generated for 'chain 'C' and resid 271 through 274' 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 355 through 358 Processing helix chain 'C' and resid 374 through 385 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 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 554 through 568 Processing helix chain 'C' and resid 579 through 582 No H-bonds generated for 'chain 'C' and resid 579 through 582' Processing helix chain 'C' and resid 596 through 608 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 713 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 765 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 43 through 48 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 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 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: 3.538A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 462 through 467 removed outlier: 4.766A pdb=" N GLU D 466 " --> pdb=" O ALA D 463 " (cutoff:3.500A) 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 525 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: 6.925A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 634 No H-bonds generated for 'chain 'D' and resid 631 through 634' 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 742 Processing helix chain 'D' and resid 749 through 766 removed outlier: 4.025A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 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 92 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 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 271 through 274 Processing helix chain 'E' and resid 282 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: 3.897A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 426 removed outlier: 3.985A 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 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 554 through 568 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 740 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 198 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 233 removed outlier: 3.506A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) 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 384 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 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 559 through 568 Processing helix chain 'F' and resid 579 through 582 No H-bonds generated for 'chain 'F' and resid 579 through 582' Processing helix chain 'F' and resid 599 through 613 removed outlier: 4.566A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' 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 65 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 109 through 111 Processing sheet with id= D, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.849A pdb=" N ARG A 113 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 181 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 150 through 154 removed outlier: 4.309A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 365 through 369 removed outlier: 3.678A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY A 245 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 347 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 641 through 644 removed outlier: 7.036A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= I, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.320A pdb=" N VAL B 39 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 103 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.167A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 150 through 154 removed outlier: 4.265A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.678A 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: 3.769A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.881A 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: 8.382A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 81 through 84 removed outlier: 8.041A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 67 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 removed outlier: 4.171A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.553A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 365 through 368 removed outlier: 6.132A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 342 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.508A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 27 through 29 Processing sheet with id= T, first strand: chain 'D' and resid 38 through 42 removed outlier: 7.511A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.510A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL D 181 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= W, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.058A pdb=" N ASP D 150 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 365 through 368 removed outlier: 8.364A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.697A 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 644 removed outlier: 8.214A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= AA, first strand: chain 'E' and resid 38 through 41 removed outlier: 7.730A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU E 41 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU E 72 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.549A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.736A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 641 through 645 removed outlier: 8.208A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= AF, first strand: chain 'F' and resid 38 through 41 removed outlier: 7.486A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 41 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU F 72 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 71 " --> pdb=" O ASP F 55 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS F 60 " --> pdb=" O SER F 101 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 113 through 115 removed outlier: 5.706A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 145 through 147 removed outlier: 3.504A pdb=" N ILE F 146 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 151 through 154 Processing sheet with id= AJ, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.581A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 641 through 644 removed outlier: 3.840A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) 1242 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: 14.43 Time building geometry restraints manager: 12.77 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: 11871 1.34 - 1.46: 6679 1.46 - 1.58: 16519 1.58 - 1.70: 25 1.70 - 1.83: 284 Bond restraints: 35378 Sorted by residual: bond pdb=" CG PRO F 44 " pdb=" CD PRO F 44 " ideal model delta sigma weight residual 1.503 1.430 0.073 3.40e-02 8.65e+02 4.63e+00 bond pdb=" C VAL D 235 " pdb=" N LYS D 236 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.47e-02 4.63e+03 3.85e+00 bond pdb=" CG1 ILE D 601 " pdb=" CD1 ILE D 601 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.37e+00 bond pdb=" O3A ATP E 902 " pdb=" PA ATP E 902 " ideal model delta sigma weight residual 1.592 1.540 0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" O3B ATP E 902 " pdb=" PB ATP E 902 " ideal model delta sigma weight residual 1.592 1.542 0.050 3.00e-02 1.11e+03 2.79e+00 ... (remaining 35373 not shown) Histogram of bond angle deviations from ideal: 95.23 - 104.17: 706 104.17 - 113.11: 19790 113.11 - 122.05: 21141 122.05 - 130.99: 6089 130.99 - 139.93: 106 Bond angle restraints: 47832 Sorted by residual: angle pdb=" N PRO F 44 " pdb=" CD PRO F 44 " pdb=" CG PRO F 44 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO F 44 " pdb=" N PRO F 44 " pdb=" CD PRO F 44 " ideal model delta sigma weight residual 112.00 104.60 7.40 1.40e+00 5.10e-01 2.79e+01 angle pdb=" C VAL D 235 " pdb=" N LYS D 236 " pdb=" CA LYS D 236 " ideal model delta sigma weight residual 120.68 127.86 -7.18 1.52e+00 4.33e-01 2.23e+01 angle pdb=" C ILE E 309 " pdb=" CA ILE E 309 " pdb=" CB ILE E 309 " ideal model delta sigma weight residual 110.95 105.66 5.29 1.48e+00 4.57e-01 1.28e+01 angle pdb=" N VAL A 165 " pdb=" CA VAL A 165 " pdb=" C VAL A 165 " ideal model delta sigma weight residual 106.21 109.89 -3.68 1.07e+00 8.73e-01 1.18e+01 ... (remaining 47827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 21418 32.83 - 65.65: 570 65.65 - 98.48: 63 98.48 - 131.31: 3 131.31 - 164.14: 6 Dihedral angle restraints: 22060 sinusoidal: 9358 harmonic: 12702 Sorted by residual: dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 104.13 -164.14 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+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 81.11 -141.11 1 2.00e+01 2.50e-03 4.27e+01 ... (remaining 22057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3982 0.048 - 0.097: 1096 0.097 - 0.145: 283 0.145 - 0.193: 10 0.193 - 0.242: 2 Chirality restraints: 5373 Sorted by residual: chirality pdb=" CB ILE A 300 " pdb=" CA ILE A 300 " pdb=" CG1 ILE A 300 " pdb=" CG2 ILE A 300 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE F 619 " pdb=" CA ILE F 619 " pdb=" CG1 ILE F 619 " pdb=" CG2 ILE F 619 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CA ILE C 269 " pdb=" N ILE C 269 " pdb=" C ILE C 269 " pdb=" CB ILE C 269 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 5370 not shown) Planarity restraints: 6263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 773 " 0.059 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO D 774 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO D 774 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 774 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 454 " -0.015 2.00e-02 2.50e+03 1.84e-02 8.47e+00 pdb=" CG TRP B 454 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 454 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 454 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 454 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 454 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 454 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO C 545 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.036 5.00e-02 4.00e+02 ... (remaining 6260 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 212 2.51 - 3.11: 26445 3.11 - 3.70: 55610 3.70 - 4.30: 79904 4.30 - 4.90: 129552 Nonbonded interactions: 291723 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 1.912 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 904 " model vdw 1.915 2.170 nonbonded pdb=" O1B ATP B 901 " pdb="MG MG B 903 " model vdw 1.922 2.170 nonbonded pdb=" O3G ATP D 901 " pdb="MG MG D 904 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP D 901 " pdb="MG MG D 904 " model vdw 1.969 2.170 ... (remaining 291718 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 533 or (resid 534 and (name N or name CA or name C or \ name O or name CB )) or resid 535 through 545 or resid 558 through 583 or resid \ 596 through 762)) selection = (chain 'B' and (resid 23 through 507 or (resid 508 and (name N or name CA or nam \ e C or name O or name CB )) or resid 509 through 545 or resid 558 through 583 or \ resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 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 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 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 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 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 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 through \ 461 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or \ name O or name CB )) or resid 509 through 533 or (resid 534 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.880 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 85.890 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 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 : 0.006 0.073 35378 Z= 0.406 Angle : 0.756 10.176 47832 Z= 0.406 Chirality : 0.047 0.242 5373 Planarity : 0.006 0.088 6263 Dihedral : 14.961 164.136 13816 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 4366 helix: 0.71 (0.11), residues: 1960 sheet: 0.58 (0.21), residues: 609 loop : 0.15 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 454 HIS 0.012 0.002 HIS C 226 PHE 0.025 0.002 PHE A 302 TYR 0.022 0.002 TYR F 517 ARG 0.012 0.001 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 4.407 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: D 508 MET cc_start: 0.7774 (mmm) cc_final: 0.7565 (mmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.5136 time to fit residues: 168.2848 Evaluate side-chains 143 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 370 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 177 optimal weight: 0.3980 chunk 344 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 256 optimal weight: 0.9980 chunk 398 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35378 Z= 0.198 Angle : 0.568 8.799 47832 Z= 0.282 Chirality : 0.042 0.156 5373 Planarity : 0.004 0.070 6263 Dihedral : 10.969 161.256 5085 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 0.30 % Allowed : 5.50 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.03 (0.13), residues: 4366 helix: 1.22 (0.12), residues: 1961 sheet: 0.52 (0.21), residues: 610 loop : 0.31 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 454 HIS 0.006 0.001 HIS A 735 PHE 0.014 0.001 PHE A 360 TYR 0.018 0.002 TYR A 134 ARG 0.006 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 4.109 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: C 508 MET cc_start: 0.7756 (mmm) cc_final: 0.7507 (mmm) REVERT: E 550 MET cc_start: 0.7308 (ptm) cc_final: 0.7050 (ttp) outliers start: 11 outliers final: 5 residues processed: 159 average time/residue: 0.4813 time to fit residues: 126.8376 Evaluate side-chains 142 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 221 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 331 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 399 optimal weight: 1.9990 chunk 431 optimal weight: 20.0000 chunk 355 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 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** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 384 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 533 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35378 Z= 0.293 Angle : 0.583 8.363 47832 Z= 0.287 Chirality : 0.043 0.148 5373 Planarity : 0.004 0.071 6263 Dihedral : 10.626 159.438 5085 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.38 % Favored : 97.57 % Rotamer: Outliers : 0.54 % Allowed : 7.90 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.23 (0.13), residues: 4366 helix: 1.49 (0.12), residues: 1933 sheet: 0.35 (0.21), residues: 627 loop : 0.41 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 454 HIS 0.006 0.001 HIS A 735 PHE 0.017 0.001 PHE A 302 TYR 0.014 0.002 TYR A 134 ARG 0.010 0.001 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 5.168 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 611 MET cc_start: 0.4565 (tmm) cc_final: 0.4364 (tmm) REVERT: D 508 MET cc_start: 0.7143 (mmm) cc_final: 0.6874 (mmm) REVERT: E 550 MET cc_start: 0.7411 (ptm) cc_final: 0.7138 (ttp) outliers start: 20 outliers final: 12 residues processed: 151 average time/residue: 0.4435 time to fit residues: 115.6795 Evaluate side-chains 145 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 394 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 190 optimal weight: 0.0670 chunk 268 optimal weight: 0.9980 chunk 400 optimal weight: 9.9990 chunk 424 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 379 optimal weight: 40.0000 chunk 114 optimal weight: 0.0980 overall best weight: 1.3920 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35378 Z= 0.167 Angle : 0.520 7.569 47832 Z= 0.253 Chirality : 0.041 0.149 5373 Planarity : 0.004 0.069 6263 Dihedral : 10.123 157.336 5085 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Rotamer: Outliers : 0.84 % Allowed : 9.17 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.38 (0.13), residues: 4366 helix: 1.64 (0.12), residues: 1945 sheet: 0.40 (0.21), residues: 616 loop : 0.45 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 476 HIS 0.004 0.001 HIS E 183 PHE 0.016 0.001 PHE A 302 TYR 0.012 0.001 TYR A 134 ARG 0.005 0.000 ARG E 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 4.225 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: D 508 MET cc_start: 0.7238 (mmm) cc_final: 0.6952 (mmm) REVERT: E 550 MET cc_start: 0.7497 (ptm) cc_final: 0.7165 (ttp) REVERT: F 608 MET cc_start: 0.8253 (ppp) cc_final: 0.7929 (ppp) REVERT: F 611 MET cc_start: 0.6076 (ppp) cc_final: 0.5419 (mmm) outliers start: 31 outliers final: 14 residues processed: 164 average time/residue: 0.4333 time to fit residues: 124.5758 Evaluate side-chains 144 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 353 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 chunk 315 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 362 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 380 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35378 Z= 0.298 Angle : 0.584 8.585 47832 Z= 0.283 Chirality : 0.042 0.157 5373 Planarity : 0.004 0.066 6263 Dihedral : 10.095 153.542 5085 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 0.94 % Allowed : 10.43 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.38 (0.13), residues: 4366 helix: 1.66 (0.12), residues: 1942 sheet: 0.25 (0.21), residues: 627 loop : 0.49 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 551 HIS 0.005 0.001 HIS E 183 PHE 0.018 0.001 PHE A 302 TYR 0.022 0.001 TYR B 138 ARG 0.005 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 4.147 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 550 MET cc_start: 0.6545 (ptm) cc_final: 0.6154 (ttp) REVERT: D 508 MET cc_start: 0.7249 (mmm) cc_final: 0.6997 (mmm) REVERT: E 550 MET cc_start: 0.7469 (ptm) cc_final: 0.7191 (ttp) outliers start: 35 outliers final: 19 residues processed: 165 average time/residue: 0.4380 time to fit residues: 123.3943 Evaluate side-chains 150 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 142 optimal weight: 9.9990 chunk 382 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 424 optimal weight: 30.0000 chunk 352 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 overall best weight: 2.5904 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35378 Z= 0.232 Angle : 0.540 8.801 47832 Z= 0.262 Chirality : 0.042 0.148 5373 Planarity : 0.004 0.063 6263 Dihedral : 9.813 155.346 5085 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Rotamer: Outliers : 1.29 % Allowed : 11.05 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.41 (0.13), residues: 4366 helix: 1.70 (0.12), residues: 1948 sheet: 0.26 (0.21), residues: 634 loop : 0.50 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.004 0.001 HIS E 183 PHE 0.013 0.001 PHE B 152 TYR 0.012 0.001 TYR A 134 ARG 0.006 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 4.526 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: D 508 MET cc_start: 0.7296 (mmm) cc_final: 0.7081 (mmm) REVERT: E 550 MET cc_start: 0.7477 (ptm) cc_final: 0.7194 (ttp) REVERT: E 623 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (p) outliers start: 48 outliers final: 23 residues processed: 176 average time/residue: 0.4459 time to fit residues: 135.5751 Evaluate side-chains 156 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 623 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 669 ASP Chi-restraints excluded: chain E residue 750 ASN Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 409 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 242 optimal weight: 0.5980 chunk 310 optimal weight: 20.0000 chunk 240 optimal weight: 0.8980 chunk 357 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 264 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 35378 Z= 0.139 Angle : 0.525 10.029 47832 Z= 0.251 Chirality : 0.041 0.197 5373 Planarity : 0.004 0.065 6263 Dihedral : 9.382 155.187 5085 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.83 % Favored : 98.12 % Rotamer: Outliers : 0.81 % Allowed : 12.13 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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 (0.13), residues: 4366 helix: 1.75 (0.12), residues: 1955 sheet: 0.30 (0.21), residues: 637 loop : 0.53 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.003 0.001 HIS E 183 PHE 0.012 0.001 PHE A 302 TYR 0.011 0.001 TYR F 203 ARG 0.003 0.000 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 4.130 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: C 46 MET cc_start: 0.2724 (OUTLIER) cc_final: 0.1362 (mpp) REVERT: C 550 MET cc_start: 0.6355 (ptm) cc_final: 0.6088 (ttp) REVERT: D 508 MET cc_start: 0.7312 (mmm) cc_final: 0.7094 (mmm) REVERT: E 550 MET cc_start: 0.7506 (ptm) cc_final: 0.7226 (ttp) REVERT: E 623 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8515 (p) outliers start: 30 outliers final: 21 residues processed: 161 average time/residue: 0.4442 time to fit residues: 122.5888 Evaluate side-chains 153 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 261 optimal weight: 0.0000 chunk 168 optimal weight: 0.4980 chunk 252 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35378 Z= 0.158 Angle : 0.529 12.759 47832 Z= 0.251 Chirality : 0.041 0.179 5373 Planarity : 0.004 0.062 6263 Dihedral : 9.241 156.260 5085 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 0.86 % Allowed : 12.32 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.54 (0.13), residues: 4366 helix: 1.79 (0.12), residues: 1956 sheet: 0.33 (0.21), residues: 637 loop : 0.57 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 551 HIS 0.003 0.001 HIS A 735 PHE 0.023 0.001 PHE C 163 TYR 0.010 0.001 TYR A 134 ARG 0.004 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 4.123 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: C 550 MET cc_start: 0.6487 (ptm) cc_final: 0.6208 (ttp) REVERT: D 508 MET cc_start: 0.7270 (mmm) cc_final: 0.7019 (mmm) REVERT: E 550 MET cc_start: 0.7455 (ptm) cc_final: 0.7189 (ttp) REVERT: E 623 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 219 MET cc_start: 0.7016 (mmm) cc_final: 0.6372 (mtt) REVERT: F 508 MET cc_start: 0.6039 (mmm) cc_final: 0.5748 (mmm) outliers start: 32 outliers final: 24 residues processed: 163 average time/residue: 0.4585 time to fit residues: 128.7618 Evaluate side-chains 156 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 384 optimal weight: 0.8980 chunk 405 optimal weight: 0.3980 chunk 369 optimal weight: 20.0000 chunk 394 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 309 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 356 optimal weight: 0.0670 chunk 372 optimal weight: 0.9990 chunk 392 optimal weight: 9.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35378 Z= 0.128 Angle : 0.516 10.273 47832 Z= 0.245 Chirality : 0.041 0.185 5373 Planarity : 0.004 0.063 6263 Dihedral : 8.921 155.756 5085 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Rotamer: Outliers : 0.70 % Allowed : 12.59 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.61 (0.13), residues: 4366 helix: 1.83 (0.12), residues: 1960 sheet: 0.42 (0.21), residues: 640 loop : 0.59 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 454 HIS 0.002 0.000 HIS E 183 PHE 0.018 0.001 PHE C 163 TYR 0.010 0.001 TYR A 134 ARG 0.005 0.000 ARG F 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 3.935 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: A 165 VAL cc_start: 0.4936 (OUTLIER) cc_final: 0.4435 (p) REVERT: C 550 MET cc_start: 0.6410 (ptm) cc_final: 0.6156 (ttp) REVERT: C 678 MET cc_start: 0.5821 (mmm) cc_final: 0.5597 (mmp) REVERT: D 508 MET cc_start: 0.7265 (mmm) cc_final: 0.7046 (mmm) REVERT: E 550 MET cc_start: 0.7512 (ptm) cc_final: 0.7261 (ttp) REVERT: F 219 MET cc_start: 0.6987 (mmm) cc_final: 0.6385 (mtt) outliers start: 26 outliers final: 23 residues processed: 153 average time/residue: 0.4445 time to fit residues: 117.8625 Evaluate side-chains 151 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 258 optimal weight: 3.9990 chunk 416 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 437 optimal weight: 7.9990 chunk 402 optimal weight: 0.0070 chunk 348 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35378 Z= 0.172 Angle : 0.529 10.965 47832 Z= 0.250 Chirality : 0.041 0.173 5373 Planarity : 0.004 0.060 6263 Dihedral : 8.880 157.163 5085 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 0.75 % Allowed : 12.70 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.66 (0.13), residues: 4366 helix: 1.88 (0.12), residues: 1962 sheet: 0.44 (0.21), residues: 642 loop : 0.63 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 551 HIS 0.002 0.001 HIS A 735 PHE 0.014 0.001 PHE C 163 TYR 0.010 0.001 TYR A 134 ARG 0.005 0.000 ARG F 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8732 Ramachandran restraints generated. 4366 Oldfield, 0 Emsley, 4366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 5.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 VAL cc_start: 0.4829 (OUTLIER) cc_final: 0.4538 (p) REVERT: C 550 MET cc_start: 0.6465 (ptm) cc_final: 0.6230 (ttp) REVERT: C 678 MET cc_start: 0.5903 (mmm) cc_final: 0.5629 (mmp) REVERT: D 508 MET cc_start: 0.7329 (mmm) cc_final: 0.7123 (mmm) REVERT: E 550 MET cc_start: 0.7420 (ptm) cc_final: 0.7192 (ttp) REVERT: E 623 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8513 (p) REVERT: F 219 MET cc_start: 0.6906 (mmm) cc_final: 0.6340 (mtt) outliers start: 28 outliers final: 24 residues processed: 159 average time/residue: 0.4489 time to fit residues: 124.0154 Evaluate side-chains 157 residues out of total 3762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 751 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 276 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 348 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 538 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.077514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052464 restraints weight = 165645.514| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.48 r_work: 0.2841 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 35378 Z= 0.356 Angle : 0.622 12.010 47832 Z= 0.301 Chirality : 0.043 0.168 5373 Planarity : 0.004 0.055 6263 Dihedral : 9.408 165.756 5085 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Rotamer: Outliers : 1.02 % Allowed : 12.46 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.97 % 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: 1.50 (0.13), residues: 4366 helix: 1.74 (0.12), residues: 1947 sheet: 0.35 (0.21), residues: 643 loop : 0.56 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.005 0.001 HIS F 226 PHE 0.015 0.002 PHE A 302 TYR 0.013 0.002 TYR A 134 ARG 0.006 0.001 ARG F 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.07 seconds wall clock time: 107 minutes 21.78 seconds (6441.78 seconds total)