Starting phenix.real_space_refine on Sun Mar 24 09:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u8t_8519/03_2024/5u8t_8519_neut_updated.pdb" } resolution = 4.9 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= 0.006 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: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 179 5.16 5 C 25736 2.51 5 N 7061 2.21 5 O 7789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 383": "NH1" <-> "NH2" Residue "2 ARG 387": "NH1" <-> "NH2" Residue "2 TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 534": "NH1" <-> "NH2" Residue "2 ARG 656": "NH1" <-> "NH2" Residue "2 PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 705": "NH1" <-> "NH2" Residue "2 TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 794": "NH1" <-> "NH2" Residue "2 ARG 808": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "2 PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 854": "NH1" <-> "NH2" Residue "2 ARG 859": "NH1" <-> "NH2" Residue "2 TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 291": "NH1" <-> "NH2" Residue "3 ARG 420": "NH1" <-> "NH2" Residue "3 ARG 435": "NH1" <-> "NH2" Residue "3 ARG 483": "NH1" <-> "NH2" Residue "3 ARG 657": "NH1" <-> "NH2" Residue "3 ARG 700": "NH1" <-> "NH2" Residue "3 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "4 ARG 451": "NH1" <-> "NH2" Residue "4 TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 499": "NH1" <-> "NH2" Residue "4 ARG 557": "NH1" <-> "NH2" Residue "4 ARG 559": "NH1" <-> "NH2" Residue "4 TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 607": "NH1" <-> "NH2" Residue "4 ARG 681": "NH1" <-> "NH2" Residue "4 TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 796": "NH1" <-> "NH2" Residue "4 ARG 827": "NH1" <-> "NH2" Residue "4 PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "5 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 407": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 460": "NH1" <-> "NH2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "6 ARG 112": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 186": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 275": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 382": "NH1" <-> "NH2" Residue "6 ARG 531": "NH1" <-> "NH2" Residue "6 ARG 691": "NH1" <-> "NH2" Residue "6 ARG 708": "NH1" <-> "NH2" Residue "6 ARG 781": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "7 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 152": "NH1" <-> "NH2" Residue "7 ARG 157": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 216": "NH1" <-> "NH2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 303": "NH1" <-> "NH2" Residue "7 ARG 400": "NH1" <-> "NH2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 22": "NH1" <-> "NH2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 135": "NH1" <-> "NH2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 226": "NH1" <-> "NH2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 398": "NH1" <-> "NH2" Residue "E TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 472": "NH1" <-> "NH2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 547": "NH1" <-> "NH2" Residue "E TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 634": "NH1" <-> "NH2" Residue "E PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40788 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4591 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 16, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "3" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4624 Classifications: {'peptide': 589} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 543} Chain breaks: 4 Chain: "4" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5318 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 23, 'PTRANS': 22, 'TRANS': 626} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4740 Classifications: {'peptide': 602} Link IDs: {'CIS': 18, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5142 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 33, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 606} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5201 Classifications: {'peptide': 660} Link IDs: {'CIS': 25, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 604} Chain breaks: 3 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 165} Chain breaks: 1 Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'CIS': 12, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 2 Chain: "E" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 Classifications: {'peptide': 553} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.97, per 1000 atoms: 0.51 Number of scatterers: 40788 At special positions: 0 Unit cell: (183.3, 182, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 179 16.00 P 23 15.00 O 7789 8.00 N 7061 7.00 C 25736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.07 Conformation dependent library (CDL) restraints added in 7.7 seconds 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9716 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 187 helices and 37 sheets defined 37.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.33 Creating SS restraints... Processing helix chain '2' and resid 202 through 215 removed outlier: 3.756A pdb=" N LEU 2 211 " --> pdb=" O ALA 2 208 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS 2 212 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 252 removed outlier: 3.578A pdb=" N ALA 2 250 " --> pdb=" O TYR 2 246 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 282 removed outlier: 4.848A pdb=" N CYS 2 263 " --> pdb=" O LEU 2 260 " (cutoff:3.500A) Proline residue: 2 264 - end of helix removed outlier: 3.966A pdb=" N LEU 2 268 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE 2 270 " --> pdb=" O MET 2 267 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP 2 272 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET 2 276 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 2 281 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 439 through 441 No H-bonds generated for 'chain '2' and resid 439 through 441' Processing helix chain '2' and resid 478 through 488 removed outlier: 3.801A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 491 through 500 removed outlier: 4.200A pdb=" N ILE 2 494 " --> pdb=" O ARG 2 491 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE 2 497 " --> pdb=" O ILE 2 494 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER 2 500 " --> pdb=" O ILE 2 497 " (cutoff:3.500A) Processing helix chain '2' and resid 509 through 520 removed outlier: 3.695A pdb=" N THR 2 513 " --> pdb=" O ARG 2 509 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA 2 514 " --> pdb=" O ASP 2 510 " (cutoff:3.500A) Processing helix chain '2' and resid 549 through 559 removed outlier: 3.546A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR 2 555 " --> pdb=" O GLN 2 551 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 618 through 626 removed outlier: 4.395A pdb=" N MET 2 624 " --> pdb=" O HIS 2 621 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 2 626 " --> pdb=" O ALA 2 623 " (cutoff:3.500A) Processing helix chain '2' and resid 663 through 665 No H-bonds generated for 'chain '2' and resid 663 through 665' Processing helix chain '2' and resid 671 through 674 No H-bonds generated for 'chain '2' and resid 671 through 674' Processing helix chain '2' and resid 689 through 702 removed outlier: 3.593A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 771 Processing helix chain '2' and resid 780 through 794 removed outlier: 3.656A pdb=" N ASP 2 784 " --> pdb=" O GLN 2 780 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS 2 785 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER 2 787 " --> pdb=" O MET 2 783 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 824 removed outlier: 3.851A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG 2 815 " --> pdb=" O GLU 2 811 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER 2 819 " --> pdb=" O ARG 2 815 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE 2 820 " --> pdb=" O ILE 2 816 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 846 removed outlier: 3.728A pdb=" N ALA 2 837 " --> pdb=" O ASP 2 833 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP 2 843 " --> pdb=" O LYS 2 839 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 863 removed outlier: 3.952A pdb=" N LEU 2 857 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG 2 859 " --> pdb=" O GLN 2 856 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE 2 861 " --> pdb=" O ARG 2 858 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA 2 862 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 31 removed outlier: 3.783A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 52 removed outlier: 4.485A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 105 removed outlier: 3.967A pdb=" N ARG 3 104 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 116 removed outlier: 4.595A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 122 through 135 Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 345 through 354 removed outlier: 3.602A pdb=" N ASN 3 349 " --> pdb=" O PHE 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 367 removed outlier: 3.817A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 424 removed outlier: 3.635A pdb=" N VAL 3 422 " --> pdb=" O LEU 3 418 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 480 through 490 removed outlier: 3.992A pdb=" N VAL 3 484 " --> pdb=" O ASP 3 480 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 538 through 541 No H-bonds generated for 'chain '3' and resid 538 through 541' Processing helix chain '3' and resid 555 through 569 removed outlier: 3.980A pdb=" N SER 3 560 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 3 565 " --> pdb=" O ILE 3 561 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 653 through 665 removed outlier: 3.807A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 687 removed outlier: 3.757A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 3 680 " --> pdb=" O ILE 3 676 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 removed outlier: 3.665A pdb=" N LEU 3 705 " --> pdb=" O THR 3 701 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 737 removed outlier: 3.635A pdb=" N ARG 3 734 " --> pdb=" O ALA 3 730 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) Processing helix chain '4' and resid 190 through 193 No H-bonds generated for 'chain '4' and resid 190 through 193' Processing helix chain '4' and resid 227 through 236 removed outlier: 3.971A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 257 through 263 removed outlier: 3.533A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 282 removed outlier: 3.781A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP 4 278 " --> pdb=" O GLN 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 284 through 287 No H-bonds generated for 'chain '4' and resid 284 through 287' Processing helix chain '4' and resid 295 through 298 No H-bonds generated for 'chain '4' and resid 295 through 298' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 507 through 514 Processing helix chain '4' and resid 516 through 526 removed outlier: 4.426A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 4 521 " --> pdb=" O LEU 4 518 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU 4 522 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 544 removed outlier: 3.507A pdb=" N LEU 4 544 " --> pdb=" O ILE 4 540 " (cutoff:3.500A) Processing helix chain '4' and resid 574 through 584 removed outlier: 3.994A pdb=" N LYS 4 583 " --> pdb=" O GLN 4 579 " (cutoff:3.500A) Processing helix chain '4' and resid 609 through 611 No H-bonds generated for 'chain '4' and resid 609 through 611' Processing helix chain '4' and resid 620 through 624 removed outlier: 3.622A pdb=" N SER 4 624 " --> pdb=" O ALA 4 620 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 620 through 624' Processing helix chain '4' and resid 645 through 648 No H-bonds generated for 'chain '4' and resid 645 through 648' Processing helix chain '4' and resid 690 through 692 No H-bonds generated for 'chain '4' and resid 690 through 692' Processing helix chain '4' and resid 696 through 699 No H-bonds generated for 'chain '4' and resid 696 through 699' Processing helix chain '4' and resid 714 through 724 removed outlier: 5.225A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 756 removed outlier: 3.782A pdb=" N LYS 4 755 " --> pdb=" O ILE 4 751 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) Processing helix chain '4' and resid 765 through 778 removed outlier: 4.405A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 4 772 " --> pdb=" O THR 4 768 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 775 " --> pdb=" O VAL 4 771 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY 4 776 " --> pdb=" O ARG 4 772 " (cutoff:3.500A) Processing helix chain '4' and resid 799 through 803 removed outlier: 4.098A pdb=" N ARG 4 803 " --> pdb=" O GLU 4 799 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 799 through 803' Processing helix chain '4' and resid 806 through 809 No H-bonds generated for 'chain '4' and resid 806 through 809' Processing helix chain '4' and resid 811 through 813 No H-bonds generated for 'chain '4' and resid 811 through 813' Processing helix chain '4' and resid 822 through 833 removed outlier: 3.967A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 858 through 875 Processing helix chain '4' and resid 883 through 888 Processing helix chain '4' and resid 900 through 911 Processing helix chain '5' and resid 22 through 37 Processing helix chain '5' and resid 45 through 54 removed outlier: 3.593A pdb=" N ARG 5 51 " --> pdb=" O ARG 5 47 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 79 Processing helix chain '5' and resid 83 through 99 removed outlier: 4.083A pdb=" N ILE 5 87 " --> pdb=" O SER 5 84 " (cutoff:3.500A) Proline residue: 5 88 - end of helix removed outlier: 3.830A pdb=" N ALA 5 93 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR 5 95 " --> pdb=" O THR 5 92 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA 5 98 " --> pdb=" O THR 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 362 removed outlier: 3.747A pdb=" N GLU 5 355 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN 5 359 " --> pdb=" O GLU 5 356 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU 5 360 " --> pdb=" O PHE 5 357 " (cutoff:3.500A) Processing helix chain '5' and resid 366 through 374 Processing helix chain '5' and resid 382 through 392 removed outlier: 4.243A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU 5 391 " --> pdb=" O ALA 5 387 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU 5 392 " --> pdb=" O ILE 5 388 " (cutoff:3.500A) Processing helix chain '5' and resid 422 through 432 removed outlier: 4.267A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 496 removed outlier: 3.892A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) Processing helix chain '5' and resid 528 through 531 removed outlier: 3.979A pdb=" N ASP 5 531 " --> pdb=" O GLY 5 528 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 528 through 531' Processing helix chain '5' and resid 545 through 549 Processing helix chain '5' and resid 564 through 576 removed outlier: 3.556A pdb=" N ILE 5 568 " --> pdb=" O ARG 5 564 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE 5 573 " --> pdb=" O ALA 5 569 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN 5 574 " --> pdb=" O ASN 5 570 " (cutoff:3.500A) Processing helix chain '5' and resid 580 through 583 No H-bonds generated for 'chain '5' and resid 580 through 583' Processing helix chain '5' and resid 587 through 591 Processing helix chain '5' and resid 597 through 608 removed outlier: 3.769A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 639 removed outlier: 3.690A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU 5 637 " --> pdb=" O LEU 5 633 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU 5 639 " --> pdb=" O ILE 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 3.646A pdb=" N GLU 5 654 " --> pdb=" O ILE 5 650 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 691 removed outlier: 4.039A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA 5 686 " --> pdb=" O ARG 5 682 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER 5 687 " --> pdb=" O LEU 5 683 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 136 through 141 Processing helix chain '6' and resid 155 through 162 removed outlier: 3.802A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 165 through 172 removed outlier: 3.543A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 191 Proline residue: 6 179 - end of helix removed outlier: 3.588A pdb=" N LYS 6 183 " --> pdb=" O PRO 6 179 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 513 through 521 removed outlier: 3.804A pdb=" N GLU 6 518 " --> pdb=" O ASN 6 514 " (cutoff:3.500A) Processing helix chain '6' and resid 525 through 531 removed outlier: 3.580A pdb=" N VAL 6 530 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 551 Processing helix chain '6' and resid 582 through 589 Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 654 through 657 No H-bonds generated for 'chain '6' and resid 654 through 657' Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 706 No H-bonds generated for 'chain '6' and resid 703 through 706' Processing helix chain '6' and resid 721 through 727 Processing helix chain '6' and resid 730 through 735 Processing helix chain '6' and resid 748 through 758 Processing helix chain '6' and resid 768 through 784 removed outlier: 3.648A pdb=" N LYS 6 776 " --> pdb=" O LEU 6 773 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS 6 782 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP 6 783 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP 6 784 " --> pdb=" O ARG 6 781 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 814 removed outlier: 3.732A pdb=" N SER 6 802 " --> pdb=" O GLN 6 799 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU 6 806 " --> pdb=" O MET 6 803 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU 6 808 " --> pdb=" O ARG 6 805 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 836 removed outlier: 4.152A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '6' and resid 912 through 923 removed outlier: 3.869A pdb=" N VAL 6 917 " --> pdb=" O MET 6 913 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE 6 920 " --> pdb=" O ILE 6 916 " (cutoff:3.500A) Processing helix chain '6' and resid 935 through 938 No H-bonds generated for 'chain '6' and resid 935 through 938' Processing helix chain '6' and resid 940 through 947 removed outlier: 4.154A pdb=" N GLU 6 945 " --> pdb=" O LEU 6 941 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN 6 946 " --> pdb=" O LEU 6 942 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP 6 947 " --> pdb=" O GLN 6 943 " (cutoff:3.500A) Processing helix chain '6' and resid 952 through 955 No H-bonds generated for 'chain '6' and resid 952 through 955' Processing helix chain '6' and resid 959 through 963 Processing helix chain '6' and resid 965 through 968 No H-bonds generated for 'chain '6' and resid 965 through 968' Processing helix chain '7' and resid 14 through 24 removed outlier: 4.036A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 71 removed outlier: 3.726A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN 7 68 " --> pdb=" O MET 7 64 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 91 Processing helix chain '7' and resid 103 through 107 Processing helix chain '7' and resid 112 through 114 No H-bonds generated for 'chain '7' and resid 112 through 114' Processing helix chain '7' and resid 119 through 124 removed outlier: 3.515A pdb=" N ASP 7 122 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN 7 124 " --> pdb=" O ILE 7 121 " (cutoff:3.500A) Processing helix chain '7' and resid 140 through 157 removed outlier: 3.861A pdb=" N ARG 7 157 " --> pdb=" O MET 7 153 " (cutoff:3.500A) Processing helix chain '7' and resid 217 through 219 No H-bonds generated for 'chain '7' and resid 217 through 219' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 396 through 400 Processing helix chain '7' and resid 402 through 407 Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.805A pdb=" N ALA 7 431 " --> pdb=" O ASP 7 427 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 476 removed outlier: 3.658A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) Processing helix chain '7' and resid 534 through 540 Processing helix chain '7' and resid 608 through 616 Processing helix chain '7' and resid 618 through 621 No H-bonds generated for 'chain '7' and resid 618 through 621' Processing helix chain '7' and resid 635 through 645 removed outlier: 3.538A pdb=" N TYR 7 641 " --> pdb=" O LYS 7 637 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 670 removed outlier: 3.575A pdb=" N ALA 7 663 " --> pdb=" O TYR 7 659 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR 7 664 " --> pdb=" O VAL 7 660 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 7 666 " --> pdb=" O GLN 7 662 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 removed outlier: 4.084A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) Processing helix chain '7' and resid 710 through 723 removed outlier: 4.391A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 7 719 " --> pdb=" O GLU 7 715 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG 7 721 " --> pdb=" O LEU 7 717 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 7 722 " --> pdb=" O ARG 7 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.858A pdb=" N LEU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 4.041A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 75 through 103 removed outlier: 3.984A pdb=" N LEU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.658A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.709A pdb=" N GLU A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.741A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.631A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 141 through 161 removed outlier: 4.304A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 removed outlier: 3.870A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.762A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.847A pdb=" N ASP C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.782A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.613A pdb=" N LYS C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 119 through 138 removed outlier: 3.897A pdb=" N GLU C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 171 through 191 removed outlier: 3.904A pdb=" N TYR C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.598A pdb=" N PHE D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 103 removed outlier: 4.911A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 162 removed outlier: 3.519A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 142 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 198 Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 279 through 287 removed outlier: 4.423A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 17 removed outlier: 3.564A pdb=" N ARG E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 4.568A pdb=" N CYS E 40 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR E 42 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET E 44 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 removed outlier: 3.924A pdb=" N ARG E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 156 through 159 No H-bonds generated for 'chain 'E' and resid 156 through 159' Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.740A pdb=" N GLU E 239 " --> pdb=" O GLY E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.433A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 301 Proline residue: E 293 - end of helix removed outlier: 4.759A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 348 removed outlier: 3.860A pdb=" N ALA E 346 " --> pdb=" O ASN E 342 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS E 347 " --> pdb=" O TYR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 364 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'E' and resid 388 through 398 removed outlier: 4.962A pdb=" N ASP E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 421 through 428 removed outlier: 4.181A pdb=" N GLU E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 428 " --> pdb=" O PHE E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 433 No H-bonds generated for 'chain 'E' and resid 430 through 433' Processing helix chain 'E' and resid 464 through 484 removed outlier: 3.860A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 514 removed outlier: 3.639A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN E 500 " --> pdb=" O ILE E 496 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 556 Processing helix chain 'E' and resid 605 through 613 removed outlier: 3.644A pdb=" N GLN E 610 " --> pdb=" O SER E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 645 removed outlier: 3.642A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 320 through 323 Processing sheet with id= B, first strand: chain '2' and resid 331 through 333 Processing sheet with id= C, first strand: chain '2' and resid 679 through 681 removed outlier: 6.086A pdb=" N ILE 2 646 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU 2 541 " --> pdb=" O ILE 2 646 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA 2 648 " --> pdb=" O LEU 2 541 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 579 through 582 Processing sheet with id= E, first strand: chain '3' and resid 179 through 185 removed outlier: 3.920A pdb=" N LEU 3 320 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 210 through 213 removed outlier: 3.827A pdb=" N THR 3 242 " --> pdb=" O TYR 3 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 253 through 258 Processing sheet with id= H, first strand: chain '3' and resid 545 through 549 removed outlier: 3.854A pdb=" N LEU 3 545 " --> pdb=" O ASN 3 404 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N MET 3 407 " --> pdb=" O VAL 3 512 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA 3 514 " --> pdb=" O MET 3 407 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA 3 516 " --> pdb=" O GLY 3 409 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 494 through 496 Processing sheet with id= J, first strand: chain '4' and resid 339 through 342 Processing sheet with id= K, first strand: chain '4' and resid 344 through 346 Processing sheet with id= L, first strand: chain '4' and resid 414 through 417 removed outlier: 4.147A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 439 through 442 Processing sheet with id= N, first strand: chain '4' and resid 705 through 707 removed outlier: 8.841A pdb=" N TYR 4 706 " --> pdb=" O ASN 4 563 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU 4 566 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA 4 673 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 653 through 656 Processing sheet with id= P, first strand: chain '5' and resid 60 through 62 removed outlier: 7.568A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '5' and resid 189 through 193 removed outlier: 6.022A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '5' and resid 273 through 275 removed outlier: 3.675A pdb=" N LEU 5 258 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS 5 257 " --> pdb=" O SER 5 168 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '5' and resid 292 through 294 Processing sheet with id= T, first strand: chain '5' and resid 297 through 301 Processing sheet with id= U, first strand: chain '5' and resid 411 through 413 removed outlier: 7.117A pdb=" N VAL 5 519 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE 5 479 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 501 through 503 Processing sheet with id= W, first strand: chain '6' and resid 301 through 303 Processing sheet with id= X, first strand: chain '6' and resid 378 through 380 removed outlier: 4.305A pdb=" N ARG 6 360 " --> pdb=" O ARG 6 296 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG 6 296 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLN 6 362 " --> pdb=" O VAL 6 294 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL 6 294 " --> pdb=" O GLN 6 362 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '6' and resid 403 through 405 Processing sheet with id= Z, first strand: chain '6' and resid 635 through 639 removed outlier: 6.580A pdb=" N SER 6 677 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE 6 638 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU 6 679 " --> pdb=" O ILE 6 638 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain '7' and resid 78 through 81 Processing sheet with id= AB, first strand: chain '7' and resid 237 through 243 removed outlier: 4.002A pdb=" N GLN 7 237 " --> pdb=" O PHE 7 355 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE 7 355 " --> pdb=" O GLN 7 237 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '7' and resid 244 through 246 removed outlier: 3.684A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '7' and resid 268 through 270 removed outlier: 4.314A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR 7 260 " --> pdb=" O VAL 7 269 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '7' and resid 520 through 523 removed outlier: 6.331A pdb=" N SER 7 562 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE 7 523 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU 7 564 " --> pdb=" O ILE 7 523 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'B' and resid 24 through 28 Processing sheet with id= AG, first strand: chain 'C' and resid 15 through 19 Processing sheet with id= AH, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.595A pdb=" N VAL E 59 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.394A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'E' and resid 567 through 571 Processing sheet with id= AK, first strand: chain 'E' and resid 410 through 414 removed outlier: 4.439A pdb=" N GLY E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 2922 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: 14.33 Time building geometry restraints manager: 19.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6864 1.32 - 1.44: 10346 1.44 - 1.57: 23879 1.57 - 1.69: 84 1.69 - 1.82: 294 Bond restraints: 41467 Sorted by residual: bond pdb=" O3A ANP 2 901 " pdb=" PB ANP 2 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP 5 801 " pdb=" PB ANP 5 801 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O3A ANP 31001 " pdb=" PB ANP 31001 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" CA ALA 6 664 " pdb=" CB ALA 6 664 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.51e-02 4.39e+03 3.56e+01 bond pdb=" CA ILE 3 122 " pdb=" CB ILE 3 122 " ideal model delta sigma weight residual 1.534 1.575 -0.040 6.80e-03 2.16e+04 3.48e+01 ... (remaining 41462 not shown) Histogram of bond angle deviations from ideal: 96.78 - 105.31: 845 105.31 - 113.85: 23604 113.85 - 122.38: 23587 122.38 - 130.91: 7922 130.91 - 139.44: 150 Bond angle restraints: 56108 Sorted by residual: angle pdb=" N ASP 6 839 " pdb=" CA ASP 6 839 " pdb=" C ASP 6 839 " ideal model delta sigma weight residual 111.14 129.97 -18.83 1.08e+00 8.57e-01 3.04e+02 angle pdb=" N SER E 19 " pdb=" CA SER E 19 " pdb=" C SER E 19 " ideal model delta sigma weight residual 111.14 129.70 -18.56 1.08e+00 8.57e-01 2.95e+02 angle pdb=" N ASP 7 263 " pdb=" CA ASP 7 263 " pdb=" C ASP 7 263 " ideal model delta sigma weight residual 111.14 128.10 -16.96 1.08e+00 8.57e-01 2.46e+02 angle pdb=" N ILE 6 533 " pdb=" CA ILE 6 533 " pdb=" C ILE 6 533 " ideal model delta sigma weight residual 110.74 122.94 -12.20 9.10e-01 1.21e+00 1.80e+02 angle pdb=" N VAL 2 846 " pdb=" CA VAL 2 846 " pdb=" C VAL 2 846 " ideal model delta sigma weight residual 110.42 122.79 -12.37 9.60e-01 1.09e+00 1.66e+02 ... (remaining 56103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 24551 32.72 - 65.44: 890 65.44 - 98.16: 61 98.16 - 130.89: 1 130.89 - 163.61: 3 Dihedral angle restraints: 25506 sinusoidal: 10573 harmonic: 14933 Sorted by residual: dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 120.49 59.51 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA VAL 7 257 " pdb=" C VAL 7 257 " pdb=" N ILE 7 258 " pdb=" CA ILE 7 258 " ideal model delta harmonic sigma weight residual 0.00 40.36 -40.36 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA VAL 6 560 " pdb=" C VAL 6 560 " pdb=" N GLU 6 561 " pdb=" CA GLU 6 561 " ideal model delta harmonic sigma weight residual 0.00 -40.31 40.31 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 25503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 6146 0.120 - 0.240: 307 0.240 - 0.360: 27 0.360 - 0.480: 9 0.480 - 0.600: 3 Chirality restraints: 6492 Sorted by residual: chirality pdb=" CA ASP 6 839 " pdb=" N ASP 6 839 " pdb=" C ASP 6 839 " pdb=" CB ASP 6 839 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CA SER E 19 " pdb=" N SER E 19 " pdb=" C SER E 19 " pdb=" CB SER E 19 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" CA ASP 7 263 " pdb=" N ASP 7 263 " pdb=" C ASP 7 263 " pdb=" CB ASP 7 263 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 6489 not shown) Planarity restraints: 7133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 18 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C ASN E 18 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN E 18 " -0.020 2.00e-02 2.50e+03 pdb=" N SER E 19 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS 7 262 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C CYS 7 262 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS 7 262 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP 7 263 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 4 676 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO 4 677 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO 4 677 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO 4 677 " -0.037 5.00e-02 4.00e+02 ... (remaining 7130 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 308 2.37 - 3.00: 24459 3.00 - 3.63: 67119 3.63 - 4.27: 98582 4.27 - 4.90: 150188 Nonbonded interactions: 340656 Sorted by model distance: nonbonded pdb=" CG1 ILE D 260 " pdb=" OE2 GLU D 266 " model vdw 1.737 3.440 nonbonded pdb=" O SER 4 624 " pdb=" O GLY 4 626 " model vdw 1.754 3.040 nonbonded pdb=" CD1 ILE D 260 " pdb=" OE2 GLU D 266 " model vdw 1.784 3.460 nonbonded pdb=" O ILE E 15 " pdb=" OG SER E 19 " model vdw 1.832 2.440 nonbonded pdb=" CG1 ILE D 260 " pdb=" CD GLU D 266 " model vdw 1.875 3.670 ... (remaining 340651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.460 Check model and map are aligned: 0.700 Set scattering table: 0.420 Process input model: 107.460 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.008 0.164 41467 Z= 0.497 Angle : 1.567 23.302 56108 Z= 1.023 Chirality : 0.062 0.600 6492 Planarity : 0.005 0.069 7133 Dihedral : 16.109 163.608 15784 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.09 % Favored : 88.89 % Rotamer: Outliers : 8.25 % Allowed : 10.99 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.61 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.09), residues: 4995 helix: -3.79 (0.07), residues: 1786 sheet: -2.69 (0.17), residues: 486 loop : -2.20 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 49 HIS 0.015 0.002 HIS 5 571 PHE 0.026 0.002 PHE 5 462 TYR 0.023 0.002 TYR 3 247 ARG 0.009 0.001 ARG 6 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 595 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 247 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9067 (mmp80) REVERT: 2 567 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7060 (p) REVERT: 2 763 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9027 (pt) REVERT: 3 27 ARG cc_start: 0.9570 (tpp-160) cc_final: 0.9322 (ttp80) REVERT: 3 136 MET cc_start: 0.9366 (mmm) cc_final: 0.9046 (mmm) REVERT: 3 367 LEU cc_start: 0.9193 (mt) cc_final: 0.8919 (mt) REVERT: 3 433 THR cc_start: 0.8955 (p) cc_final: 0.8741 (t) REVERT: 3 454 GLU cc_start: 0.8695 (tp30) cc_final: 0.8490 (tm-30) REVERT: 3 475 PHE cc_start: 0.8418 (t80) cc_final: 0.8045 (t80) REVERT: 3 665 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: 3 732 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9101 (tp) REVERT: 4 271 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9243 (tt) REVERT: 4 416 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8814 (p) REVERT: 4 554 LYS cc_start: 0.7920 (mttt) cc_final: 0.7667 (mtmm) REVERT: 4 654 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8123 (mm) REVERT: 4 688 VAL cc_start: 0.4523 (OUTLIER) cc_final: 0.4076 (t) REVERT: 4 864 ASP cc_start: 0.8839 (m-30) cc_final: 0.8157 (p0) REVERT: 5 21 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8977 (t0) REVERT: 5 41 ASP cc_start: 0.9442 (m-30) cc_final: 0.9186 (t0) REVERT: 5 54 ILE cc_start: 0.9849 (OUTLIER) cc_final: 0.9586 (pt) REVERT: 5 67 HIS cc_start: 0.9428 (m170) cc_final: 0.9223 (m-70) REVERT: 5 68 LEU cc_start: 0.9798 (tt) cc_final: 0.9462 (mt) REVERT: 5 162 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9235 (tt) REVERT: 5 204 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (m) REVERT: 5 251 ILE cc_start: 0.9412 (pt) cc_final: 0.8790 (mt) REVERT: 5 348 MET cc_start: 0.4260 (OUTLIER) cc_final: 0.2491 (ttm) REVERT: 5 426 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9203 (mm) REVERT: 5 462 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: 5 502 ILE cc_start: 0.9275 (mt) cc_final: 0.8955 (mm) REVERT: 5 513 LEU cc_start: 0.9169 (pp) cc_final: 0.8845 (tt) REVERT: 5 520 LEU cc_start: 0.9179 (tt) cc_final: 0.8516 (mt) REVERT: 5 526 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (pp) REVERT: 5 595 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.7643 (p) REVERT: 5 599 MET cc_start: 0.9167 (tpp) cc_final: 0.8689 (mmt) REVERT: 5 689 MET cc_start: 0.9087 (mmm) cc_final: 0.8861 (tpt) REVERT: 6 384 ASP cc_start: 0.9566 (t0) cc_final: 0.8894 (p0) REVERT: 6 387 GLU cc_start: 0.9182 (tp30) cc_final: 0.8947 (mm-30) REVERT: 6 550 GLN cc_start: 0.9495 (mt0) cc_final: 0.9049 (tp-100) REVERT: 6 551 MET cc_start: 0.8936 (mtp) cc_final: 0.8562 (tpt) REVERT: 6 629 MET cc_start: 0.7703 (ttp) cc_final: 0.7129 (tpt) REVERT: 6 656 MET cc_start: 0.9307 (mmm) cc_final: 0.9004 (mmm) REVERT: 6 662 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6883 (p) REVERT: 6 699 LEU cc_start: 0.9036 (mp) cc_final: 0.8657 (mt) REVERT: 6 709 PHE cc_start: 0.7745 (m-10) cc_final: 0.7118 (m-10) REVERT: 6 720 ASN cc_start: 0.9627 (t0) cc_final: 0.9040 (m110) REVERT: 6 752 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.9032 (ttm-80) REVERT: 6 794 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7749 (mmt180) REVERT: 6 803 MET cc_start: 0.9045 (tpp) cc_final: 0.8834 (mmm) REVERT: 6 824 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9345 (tp) REVERT: 6 831 LEU cc_start: 0.9607 (mt) cc_final: 0.9275 (mm) REVERT: 6 967 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.3958 (ppt90) REVERT: 7 86 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8816 (tt) REVERT: 7 125 MET cc_start: 0.8999 (ttm) cc_final: 0.8681 (tmm) REVERT: 7 147 ARG cc_start: 0.8796 (mtt-85) cc_final: 0.8431 (tpp80) REVERT: 7 372 THR cc_start: 0.9017 (p) cc_final: 0.8726 (p) REVERT: 7 454 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8536 (mm) REVERT: 7 458 LEU cc_start: 0.9230 (mt) cc_final: 0.8880 (mt) REVERT: 7 506 MET cc_start: 0.8304 (mmm) cc_final: 0.8091 (ppp) REVERT: 7 521 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8966 (p) REVERT: 7 527 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.9034 (t0) REVERT: A 15 ARG cc_start: 0.9731 (ptm160) cc_final: 0.9335 (ptm-80) REVERT: A 79 MET cc_start: 0.9424 (mmm) cc_final: 0.9080 (mmm) REVERT: A 104 ASN cc_start: 0.9470 (OUTLIER) cc_final: 0.9194 (p0) REVERT: A 149 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (tt) REVERT: A 151 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 164 ASP cc_start: 0.9648 (m-30) cc_final: 0.9401 (t0) REVERT: A 204 TYR cc_start: 0.9178 (m-80) cc_final: 0.8800 (m-10) REVERT: B 8 GLN cc_start: 0.9313 (pt0) cc_final: 0.8596 (tp40) REVERT: B 147 ASP cc_start: 0.9568 (t0) cc_final: 0.9363 (t0) REVERT: B 160 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9307 (tt) REVERT: B 169 GLN cc_start: 0.8846 (mt0) cc_final: 0.8267 (pm20) REVERT: C 4 TYR cc_start: 0.8590 (m-10) cc_final: 0.8283 (m-80) REVERT: C 8 ASP cc_start: 0.9528 (m-30) cc_final: 0.9169 (m-30) REVERT: C 126 GLU cc_start: 0.9765 (tp30) cc_final: 0.9397 (tp30) REVERT: C 172 MET cc_start: 0.9687 (ptm) cc_final: 0.9302 (tmm) REVERT: C 184 TYR cc_start: 0.9556 (m-80) cc_final: 0.9282 (m-80) REVERT: D 64 MET cc_start: 0.9674 (mmm) cc_final: 0.9446 (tpp) REVERT: D 93 MET cc_start: 0.9741 (mmp) cc_final: 0.9327 (mmm) REVERT: D 142 SER cc_start: 0.9589 (t) cc_final: 0.8743 (t) REVERT: E 32 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8476 (p) REVERT: E 34 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8725 (mt) REVERT: E 40 CYS cc_start: 0.9259 (m) cc_final: 0.8849 (p) REVERT: E 44 MET cc_start: 0.9826 (ptm) cc_final: 0.9536 (ptt) REVERT: E 267 LEU cc_start: 0.9440 (mt) cc_final: 0.9209 (pp) REVERT: E 284 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7031 (p90) REVERT: E 366 MET cc_start: 0.9599 (mtt) cc_final: 0.9080 (mtt) REVERT: E 387 GLU cc_start: 0.9837 (mm-30) cc_final: 0.9578 (tp30) REVERT: E 407 ASP cc_start: 0.9226 (m-30) cc_final: 0.8315 (t0) REVERT: E 485 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8906 (t0) REVERT: E 497 GLN cc_start: 0.9745 (mt0) cc_final: 0.9502 (tp-100) REVERT: E 536 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 537 ASP cc_start: 0.9257 (m-30) cc_final: 0.8672 (p0) outliers start: 371 outliers final: 96 residues processed: 911 average time/residue: 0.5237 time to fit residues: 770.9879 Evaluate side-chains 514 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 383 time to evaluate : 4.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 427 optimal weight: 0.9990 chunk 383 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 396 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 459 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 2 561 HIS 2 615 GLN 2 641 GLN 2 651 ASN ** 2 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 349 ASN ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 564 HIS ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 400 GLN 4 447 ASN 4 582 HIS ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN ** 5 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 583 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 6 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 326 HIS 7 543 GLN 7 544 GLN 7 585 ASN 7 615 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 41467 Z= 0.292 Angle : 0.970 18.479 56108 Z= 0.504 Chirality : 0.051 0.368 6492 Planarity : 0.006 0.065 7133 Dihedral : 10.978 176.431 5773 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 33.62 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.67 % Favored : 90.43 % Rotamer: Outliers : 0.29 % Allowed : 5.43 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.81 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.35 (0.10), residues: 4995 helix: -2.46 (0.09), residues: 1885 sheet: -2.52 (0.18), residues: 530 loop : -1.89 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 551 HIS 0.013 0.002 HIS 7 112 PHE 0.034 0.002 PHE 5 197 TYR 0.030 0.002 TYR 7 411 ARG 0.015 0.001 ARG 3 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 477 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9306 (ptp) cc_final: 0.9098 (ptm) REVERT: 2 541 LEU cc_start: 0.9625 (tp) cc_final: 0.9324 (tp) REVERT: 2 612 MET cc_start: 0.8695 (mtm) cc_final: 0.7579 (mtp) REVERT: 2 613 ASN cc_start: 0.8589 (m-40) cc_final: 0.8292 (m-40) REVERT: 2 681 CYS cc_start: 0.8602 (m) cc_final: 0.8269 (m) REVERT: 3 136 MET cc_start: 0.9423 (mmm) cc_final: 0.9036 (mmm) REVERT: 3 183 GLU cc_start: 0.9340 (pm20) cc_final: 0.8947 (pm20) REVERT: 3 454 GLU cc_start: 0.8726 (tp30) cc_final: 0.8440 (tm-30) REVERT: 3 475 PHE cc_start: 0.8404 (t80) cc_final: 0.8108 (t80) REVERT: 3 479 THR cc_start: 0.8671 (p) cc_final: 0.8279 (p) REVERT: 3 551 ASP cc_start: 0.7257 (t70) cc_final: 0.6729 (m-30) REVERT: 4 271 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9275 (tt) REVERT: 4 272 MET cc_start: 0.9428 (mmp) cc_final: 0.9117 (tpp) REVERT: 4 382 MET cc_start: 0.9386 (ttt) cc_final: 0.9039 (ttm) REVERT: 4 554 LYS cc_start: 0.7539 (mttt) cc_final: 0.7211 (tptt) REVERT: 4 614 LEU cc_start: 0.8814 (mm) cc_final: 0.8445 (tp) REVERT: 4 651 GLN cc_start: 0.8672 (mt0) cc_final: 0.8026 (mp10) REVERT: 4 661 ILE cc_start: 0.7599 (mm) cc_final: 0.7348 (mm) REVERT: 4 682 TYR cc_start: 0.8482 (p90) cc_final: 0.8276 (p90) REVERT: 4 801 MET cc_start: 0.8980 (ttm) cc_final: 0.8644 (mtp) REVERT: 4 902 ASP cc_start: 0.8886 (m-30) cc_final: 0.8424 (p0) REVERT: 5 41 ASP cc_start: 0.9534 (m-30) cc_final: 0.9085 (t0) REVERT: 5 48 ASP cc_start: 0.9433 (m-30) cc_final: 0.9210 (t0) REVERT: 5 57 LYS cc_start: 0.9607 (mptt) cc_final: 0.9342 (mmtt) REVERT: 5 68 LEU cc_start: 0.9737 (tt) cc_final: 0.9418 (mt) REVERT: 5 252 ASP cc_start: 0.7709 (t0) cc_final: 0.7319 (t0) REVERT: 5 260 GLU cc_start: 0.8830 (pt0) cc_final: 0.8540 (pt0) REVERT: 5 342 ILE cc_start: 0.8539 (pt) cc_final: 0.8290 (pt) REVERT: 5 404 MET cc_start: 0.6524 (ptp) cc_final: 0.6129 (ppp) REVERT: 5 409 ASP cc_start: 0.7517 (t0) cc_final: 0.7196 (t0) REVERT: 5 410 ILE cc_start: 0.8133 (pt) cc_final: 0.7875 (pt) REVERT: 5 509 ILE cc_start: 0.9265 (pt) cc_final: 0.8994 (tp) REVERT: 5 552 MET cc_start: 0.8442 (tpt) cc_final: 0.8097 (tpp) REVERT: 5 576 HIS cc_start: 0.9013 (m90) cc_final: 0.8773 (m90) REVERT: 5 599 MET cc_start: 0.9049 (tpp) cc_final: 0.8571 (mmt) REVERT: 6 384 ASP cc_start: 0.9481 (t0) cc_final: 0.8625 (p0) REVERT: 6 519 MET cc_start: 0.9586 (mtt) cc_final: 0.8920 (mtp) REVERT: 6 551 MET cc_start: 0.9007 (mtp) cc_final: 0.8503 (tpt) REVERT: 6 621 TYR cc_start: 0.8304 (p90) cc_final: 0.8028 (p90) REVERT: 6 629 MET cc_start: 0.7092 (ttp) cc_final: 0.6214 (tpp) REVERT: 6 652 ILE cc_start: 0.7134 (mt) cc_final: 0.6786 (mm) REVERT: 6 699 LEU cc_start: 0.9037 (mp) cc_final: 0.8445 (mt) REVERT: 6 720 ASN cc_start: 0.9569 (t0) cc_final: 0.9255 (m110) REVERT: 6 794 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.6450 (mmt180) REVERT: 6 831 LEU cc_start: 0.9660 (mt) cc_final: 0.9360 (mt) REVERT: 7 147 ARG cc_start: 0.9060 (mtt-85) cc_final: 0.8518 (tpp80) REVERT: 7 326 HIS cc_start: 0.9478 (m-70) cc_final: 0.9274 (m90) REVERT: 7 498 MET cc_start: 0.9125 (pmm) cc_final: 0.8398 (pmm) REVERT: 7 529 MET cc_start: 0.7758 (ptt) cc_final: 0.7406 (ptt) REVERT: 7 621 MET cc_start: 0.8304 (ptm) cc_final: 0.8088 (ptt) REVERT: A 79 MET cc_start: 0.9441 (mmm) cc_final: 0.9132 (mmm) REVERT: A 115 PHE cc_start: 0.7677 (m-10) cc_final: 0.7449 (m-80) REVERT: A 164 ASP cc_start: 0.9660 (m-30) cc_final: 0.9361 (t0) REVERT: A 204 TYR cc_start: 0.9065 (m-80) cc_final: 0.8718 (m-10) REVERT: B 20 VAL cc_start: 0.9900 (m) cc_final: 0.9563 (p) REVERT: B 134 PHE cc_start: 0.8653 (m-80) cc_final: 0.8401 (m-80) REVERT: B 189 MET cc_start: 0.9724 (mmt) cc_final: 0.9442 (mmp) REVERT: C 3 TYR cc_start: 0.8687 (t80) cc_final: 0.8439 (t80) REVERT: C 16 PHE cc_start: 0.9299 (m-80) cc_final: 0.9019 (m-80) REVERT: C 48 LEU cc_start: 0.9746 (tp) cc_final: 0.9505 (tt) REVERT: C 126 GLU cc_start: 0.9748 (tp30) cc_final: 0.9420 (tp30) REVERT: D 84 MET cc_start: 0.9327 (tmm) cc_final: 0.8932 (tmm) REVERT: D 93 MET cc_start: 0.9705 (mmp) cc_final: 0.9454 (mmm) REVERT: D 142 SER cc_start: 0.9081 (t) cc_final: 0.8880 (t) REVERT: D 277 MET cc_start: 0.8939 (mtt) cc_final: 0.8406 (mpp) REVERT: E 40 CYS cc_start: 0.9329 (m) cc_final: 0.8813 (p) REVERT: E 366 MET cc_start: 0.9419 (mtt) cc_final: 0.9174 (mtt) REVERT: E 380 MET cc_start: 0.9260 (mmp) cc_final: 0.8518 (mmp) REVERT: E 387 GLU cc_start: 0.9844 (mm-30) cc_final: 0.9559 (tp30) REVERT: E 407 ASP cc_start: 0.9118 (m-30) cc_final: 0.8240 (t0) REVERT: E 537 ASP cc_start: 0.9163 (m-30) cc_final: 0.8554 (p0) outliers start: 13 outliers final: 4 residues processed: 489 average time/residue: 0.5473 time to fit residues: 440.3997 Evaluate side-chains 353 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 348 time to evaluate : 4.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 312 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 460 optimal weight: 3.9990 chunk 497 optimal weight: 8.9990 chunk 409 optimal weight: 1.9990 chunk 456 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 369 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS ** 2 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 554 ASN 3 677 ASN 4 231 ASN ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN 5 49 GLN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 561 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 6 914 ASN ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 183 HIS ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 41467 Z= 0.296 Angle : 0.893 16.052 56108 Z= 0.466 Chirality : 0.048 0.396 6492 Planarity : 0.005 0.073 7133 Dihedral : 10.340 169.123 5773 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.09 % Favored : 89.07 % Rotamer: Outliers : 0.13 % Allowed : 5.81 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.81 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 4995 helix: -1.75 (0.10), residues: 1893 sheet: -2.41 (0.18), residues: 543 loop : -1.77 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 6 939 HIS 0.013 0.002 HIS 5 560 PHE 0.024 0.002 PHE 7 93 TYR 0.022 0.002 TYR 6 174 ARG 0.022 0.001 ARG 4 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 407 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9282 (ptp) cc_final: 0.8844 (ptt) REVERT: 2 541 LEU cc_start: 0.9524 (tp) cc_final: 0.9241 (tp) REVERT: 2 609 PHE cc_start: 0.8378 (m-80) cc_final: 0.7695 (m-80) REVERT: 2 612 MET cc_start: 0.8506 (mtm) cc_final: 0.7937 (mtp) REVERT: 2 613 ASN cc_start: 0.8742 (m-40) cc_final: 0.8478 (m-40) REVERT: 2 638 THR cc_start: 0.8821 (p) cc_final: 0.8477 (p) REVERT: 2 677 PHE cc_start: 0.9161 (m-80) cc_final: 0.8919 (m-80) REVERT: 2 681 CYS cc_start: 0.8597 (m) cc_final: 0.8016 (m) REVERT: 3 136 MET cc_start: 0.9407 (mmm) cc_final: 0.8985 (mmm) REVERT: 3 183 GLU cc_start: 0.9303 (pm20) cc_final: 0.9015 (pm20) REVERT: 3 252 ASP cc_start: 0.8910 (t0) cc_final: 0.8686 (t0) REVERT: 3 406 LEU cc_start: 0.8899 (tp) cc_final: 0.8612 (pp) REVERT: 3 454 GLU cc_start: 0.8860 (tp30) cc_final: 0.8580 (tm-30) REVERT: 3 479 THR cc_start: 0.8816 (p) cc_final: 0.8382 (p) REVERT: 4 272 MET cc_start: 0.9506 (mmp) cc_final: 0.9215 (ptt) REVERT: 4 382 MET cc_start: 0.9370 (ttt) cc_final: 0.9017 (ttm) REVERT: 4 554 LYS cc_start: 0.7621 (mttt) cc_final: 0.7148 (tptt) REVERT: 4 614 LEU cc_start: 0.8767 (mm) cc_final: 0.8268 (tp) REVERT: 4 651 GLN cc_start: 0.8779 (mt0) cc_final: 0.8018 (mp10) REVERT: 4 801 MET cc_start: 0.9167 (ttm) cc_final: 0.8596 (mtp) REVERT: 4 902 ASP cc_start: 0.8961 (m-30) cc_final: 0.8457 (p0) REVERT: 5 41 ASP cc_start: 0.9537 (m-30) cc_final: 0.9088 (t0) REVERT: 5 49 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8623 (tp-100) REVERT: 5 68 LEU cc_start: 0.9756 (tt) cc_final: 0.9454 (mt) REVERT: 5 252 ASP cc_start: 0.8281 (t0) cc_final: 0.7843 (t0) REVERT: 5 278 CYS cc_start: 0.7074 (m) cc_final: 0.6809 (m) REVERT: 5 362 ARG cc_start: 0.9233 (mtt180) cc_final: 0.8989 (mtm-85) REVERT: 5 509 ILE cc_start: 0.9346 (pt) cc_final: 0.9104 (tp) REVERT: 5 511 THR cc_start: 0.8324 (p) cc_final: 0.7878 (p) REVERT: 5 552 MET cc_start: 0.8558 (tpt) cc_final: 0.8234 (mmm) REVERT: 5 576 HIS cc_start: 0.8921 (m90) cc_final: 0.8630 (m90) REVERT: 6 384 ASP cc_start: 0.9565 (t0) cc_final: 0.8782 (p0) REVERT: 6 551 MET cc_start: 0.9025 (mtp) cc_final: 0.8674 (tpt) REVERT: 6 621 TYR cc_start: 0.8284 (p90) cc_final: 0.8078 (p90) REVERT: 6 629 MET cc_start: 0.7223 (ttp) cc_final: 0.6705 (tpp) REVERT: 6 699 LEU cc_start: 0.9049 (mp) cc_final: 0.8636 (mt) REVERT: 6 720 ASN cc_start: 0.9524 (t0) cc_final: 0.9201 (m110) REVERT: 6 735 HIS cc_start: 0.8341 (m-70) cc_final: 0.8009 (m90) REVERT: 6 794 ARG cc_start: 0.7376 (mmt-90) cc_final: 0.6317 (mmt180) REVERT: 7 125 MET cc_start: 0.8577 (tmm) cc_final: 0.7993 (tmm) REVERT: 7 529 MET cc_start: 0.7868 (ptt) cc_final: 0.7531 (ptt) REVERT: A 164 ASP cc_start: 0.9655 (m-30) cc_final: 0.9371 (t0) REVERT: A 204 TYR cc_start: 0.9069 (m-80) cc_final: 0.8635 (m-10) REVERT: B 17 GLN cc_start: 0.9431 (pt0) cc_final: 0.9207 (pt0) REVERT: B 20 VAL cc_start: 0.9852 (m) cc_final: 0.9645 (p) REVERT: C 48 LEU cc_start: 0.9697 (tp) cc_final: 0.9414 (tt) REVERT: C 126 GLU cc_start: 0.9775 (tp30) cc_final: 0.9392 (tp30) REVERT: C 175 GLU cc_start: 0.9823 (tp30) cc_final: 0.9556 (tp30) REVERT: C 189 ARG cc_start: 0.9677 (ptm160) cc_final: 0.9174 (ttp80) REVERT: D 64 MET cc_start: 0.9784 (tpp) cc_final: 0.9104 (tpp) REVERT: D 84 MET cc_start: 0.9325 (tmm) cc_final: 0.8860 (tmm) REVERT: D 93 MET cc_start: 0.9838 (mmp) cc_final: 0.9400 (mmm) REVERT: D 277 MET cc_start: 0.9206 (mtt) cc_final: 0.8890 (mmt) REVERT: E 40 CYS cc_start: 0.9343 (m) cc_final: 0.8792 (p) REVERT: E 44 MET cc_start: 0.9791 (ptt) cc_final: 0.9555 (ptp) REVERT: E 362 MET cc_start: 0.9549 (tpt) cc_final: 0.9149 (tpp) REVERT: E 380 MET cc_start: 0.9148 (mmp) cc_final: 0.8545 (mmp) REVERT: E 387 GLU cc_start: 0.9834 (mm-30) cc_final: 0.9558 (tp30) REVERT: E 407 ASP cc_start: 0.9163 (m-30) cc_final: 0.8244 (t0) REVERT: E 537 ASP cc_start: 0.9144 (m-30) cc_final: 0.8485 (p0) outliers start: 6 outliers final: 2 residues processed: 413 average time/residue: 0.5175 time to fit residues: 353.6292 Evaluate side-chains 311 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 454 optimal weight: 7.9990 chunk 346 optimal weight: 0.0030 chunk 238 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 309 optimal weight: 3.9990 chunk 461 optimal weight: 6.9990 chunk 489 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 437 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN ** 6 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 175 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41467 Z= 0.209 Angle : 0.849 18.735 56108 Z= 0.435 Chirality : 0.047 0.397 6492 Planarity : 0.004 0.057 7133 Dihedral : 9.894 164.407 5773 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.75 % Favored : 90.33 % Rotamer: Outliers : 0.11 % Allowed : 4.18 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.11), residues: 4995 helix: -1.09 (0.11), residues: 1869 sheet: -2.22 (0.19), residues: 540 loop : -1.55 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 551 HIS 0.010 0.001 HIS 5 560 PHE 0.022 0.002 PHE 7 93 TYR 0.022 0.001 TYR 6 174 ARG 0.011 0.000 ARG 4 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 433 time to evaluate : 5.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9310 (ptp) cc_final: 0.9060 (ptt) REVERT: 2 541 LEU cc_start: 0.9316 (tp) cc_final: 0.9064 (tp) REVERT: 2 609 PHE cc_start: 0.8211 (m-80) cc_final: 0.7554 (m-80) REVERT: 2 612 MET cc_start: 0.8280 (mtm) cc_final: 0.7912 (mtp) REVERT: 2 681 CYS cc_start: 0.8274 (m) cc_final: 0.7768 (m) REVERT: 2 823 MET cc_start: 0.9393 (ptp) cc_final: 0.9144 (ptp) REVERT: 3 136 MET cc_start: 0.9344 (mmm) cc_final: 0.8857 (tpp) REVERT: 3 179 LEU cc_start: 0.9496 (tp) cc_final: 0.9224 (tp) REVERT: 3 183 GLU cc_start: 0.9190 (pm20) cc_final: 0.8850 (pm20) REVERT: 3 252 ASP cc_start: 0.8799 (t0) cc_final: 0.8598 (t0) REVERT: 3 384 MET cc_start: 0.8576 (tmm) cc_final: 0.8214 (tmm) REVERT: 3 406 LEU cc_start: 0.9096 (tp) cc_final: 0.8550 (pp) REVERT: 3 454 GLU cc_start: 0.8717 (tp30) cc_final: 0.8469 (tm-30) REVERT: 3 551 ASP cc_start: 0.7063 (t70) cc_final: 0.6482 (m-30) REVERT: 4 272 MET cc_start: 0.9462 (mmp) cc_final: 0.9155 (ptt) REVERT: 4 382 MET cc_start: 0.9289 (mtp) cc_final: 0.9025 (mtp) REVERT: 4 554 LYS cc_start: 0.7289 (mttt) cc_final: 0.6874 (tptt) REVERT: 4 614 LEU cc_start: 0.8691 (mm) cc_final: 0.8404 (tp) REVERT: 4 651 GLN cc_start: 0.8745 (mt0) cc_final: 0.8235 (mp10) REVERT: 4 682 TYR cc_start: 0.8379 (p90) cc_final: 0.8175 (p90) REVERT: 4 801 MET cc_start: 0.9177 (ttm) cc_final: 0.8699 (mtp) REVERT: 4 834 LYS cc_start: 0.9566 (mmtt) cc_final: 0.9241 (pptt) REVERT: 4 902 ASP cc_start: 0.9112 (m-30) cc_final: 0.8619 (p0) REVERT: 4 903 ILE cc_start: 0.8529 (mt) cc_final: 0.8058 (mm) REVERT: 5 41 ASP cc_start: 0.9577 (m-30) cc_final: 0.9000 (t0) REVERT: 5 49 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8592 (tp-100) REVERT: 5 67 HIS cc_start: 0.9298 (m90) cc_final: 0.9009 (m90) REVERT: 5 252 ASP cc_start: 0.8070 (t0) cc_final: 0.7403 (t0) REVERT: 5 278 CYS cc_start: 0.5759 (m) cc_final: 0.5505 (m) REVERT: 5 362 ARG cc_start: 0.9302 (mtt180) cc_final: 0.8998 (mtt180) REVERT: 5 393 MET cc_start: 0.8472 (mmp) cc_final: 0.8065 (mmm) REVERT: 5 404 MET cc_start: 0.6436 (ptp) cc_final: 0.6042 (ppp) REVERT: 5 509 ILE cc_start: 0.9340 (pt) cc_final: 0.9056 (tp) REVERT: 5 511 THR cc_start: 0.8269 (p) cc_final: 0.7823 (p) REVERT: 5 552 MET cc_start: 0.8576 (tpt) cc_final: 0.8181 (tpt) REVERT: 5 576 HIS cc_start: 0.8966 (m90) cc_final: 0.8567 (m90) REVERT: 6 378 ASP cc_start: 0.9357 (p0) cc_final: 0.8614 (t0) REVERT: 6 384 ASP cc_start: 0.9504 (t0) cc_final: 0.8709 (p0) REVERT: 6 519 MET cc_start: 0.9503 (mtt) cc_final: 0.8843 (mtp) REVERT: 6 550 GLN cc_start: 0.9393 (mt0) cc_final: 0.9190 (mm-40) REVERT: 6 551 MET cc_start: 0.8944 (mtp) cc_final: 0.8504 (tpt) REVERT: 6 629 MET cc_start: 0.6877 (ttp) cc_final: 0.6444 (tpp) REVERT: 6 661 ILE cc_start: 0.9269 (mt) cc_final: 0.8819 (tt) REVERT: 6 699 LEU cc_start: 0.8926 (mp) cc_final: 0.8499 (mt) REVERT: 6 720 ASN cc_start: 0.9512 (t0) cc_final: 0.9030 (m110) REVERT: 6 735 HIS cc_start: 0.8530 (m-70) cc_final: 0.8170 (m90) REVERT: 6 803 MET cc_start: 0.8905 (mmp) cc_final: 0.8475 (mmm) REVERT: 6 915 MET cc_start: 0.8036 (mmp) cc_final: 0.7738 (mmt) REVERT: 7 29 LYS cc_start: 0.6854 (tptt) cc_final: 0.6405 (tppt) REVERT: 7 376 LEU cc_start: 0.9651 (tp) cc_final: 0.9421 (tp) REVERT: 7 457 CYS cc_start: 0.6448 (t) cc_final: 0.5461 (t) REVERT: 7 458 LEU cc_start: 0.8935 (mt) cc_final: 0.8694 (tp) REVERT: 7 498 MET cc_start: 0.8553 (pmm) cc_final: 0.8016 (pmm) REVERT: A 164 ASP cc_start: 0.9720 (m-30) cc_final: 0.9361 (t0) REVERT: A 204 TYR cc_start: 0.8973 (m-80) cc_final: 0.8557 (m-10) REVERT: B 20 VAL cc_start: 0.9851 (m) cc_final: 0.9617 (p) REVERT: B 134 PHE cc_start: 0.8555 (m-80) cc_final: 0.8335 (m-80) REVERT: B 189 MET cc_start: 0.9717 (mmp) cc_final: 0.9295 (mmm) REVERT: C 126 GLU cc_start: 0.9734 (tp30) cc_final: 0.9376 (tp30) REVERT: C 134 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 175 GLU cc_start: 0.9820 (tp30) cc_final: 0.9541 (tp30) REVERT: D 68 LYS cc_start: 0.9714 (ptpp) cc_final: 0.9419 (ptmm) REVERT: D 93 MET cc_start: 0.9814 (mmp) cc_final: 0.9332 (mmm) REVERT: D 218 MET cc_start: 0.9376 (mmm) cc_final: 0.9155 (mmm) REVERT: D 220 ASP cc_start: 0.9588 (m-30) cc_final: 0.8990 (m-30) REVERT: D 277 MET cc_start: 0.9066 (mtt) cc_final: 0.8814 (mmm) REVERT: E 40 CYS cc_start: 0.9279 (m) cc_final: 0.8700 (p) REVERT: E 44 MET cc_start: 0.9775 (ptt) cc_final: 0.9529 (ptp) REVERT: E 362 MET cc_start: 0.9518 (tpt) cc_final: 0.8912 (tpt) REVERT: E 366 MET cc_start: 0.9391 (mtt) cc_final: 0.9028 (mmm) REVERT: E 380 MET cc_start: 0.9131 (mmp) cc_final: 0.8130 (mmp) REVERT: E 387 GLU cc_start: 0.9807 (mm-30) cc_final: 0.9543 (tp30) REVERT: E 407 ASP cc_start: 0.9109 (m-30) cc_final: 0.8193 (t0) REVERT: E 537 ASP cc_start: 0.9259 (m-30) cc_final: 0.8700 (p0) outliers start: 5 outliers final: 2 residues processed: 438 average time/residue: 0.5047 time to fit residues: 369.7437 Evaluate side-chains 337 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 335 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 407 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 364 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 417 optimal weight: 5.9990 chunk 338 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 439 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 90 ASN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 41467 Z= 0.214 Angle : 0.821 18.757 56108 Z= 0.421 Chirality : 0.046 0.392 6492 Planarity : 0.004 0.111 7133 Dihedral : 9.716 164.791 5773 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.13 % Favored : 89.99 % Rotamer: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.89 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 4995 helix: -0.79 (0.11), residues: 1872 sheet: -2.14 (0.19), residues: 565 loop : -1.51 (0.13), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.017 0.001 HIS B 6 PHE 0.021 0.002 PHE 3 421 TYR 0.022 0.001 TYR 6 828 ARG 0.012 0.000 ARG 4 909 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 4.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9321 (ptp) cc_final: 0.9084 (ptt) REVERT: 2 609 PHE cc_start: 0.8227 (m-80) cc_final: 0.7550 (m-80) REVERT: 2 612 MET cc_start: 0.8293 (mtm) cc_final: 0.8065 (mtp) REVERT: 2 640 LEU cc_start: 0.8922 (tp) cc_final: 0.8665 (tt) REVERT: 2 677 PHE cc_start: 0.8990 (m-80) cc_final: 0.8617 (m-80) REVERT: 3 136 MET cc_start: 0.9361 (mmm) cc_final: 0.9000 (mmm) REVERT: 3 179 LEU cc_start: 0.9464 (tp) cc_final: 0.9212 (tp) REVERT: 3 183 GLU cc_start: 0.9161 (pm20) cc_final: 0.8859 (pm20) REVERT: 3 252 ASP cc_start: 0.8772 (t0) cc_final: 0.8538 (t0) REVERT: 3 367 LEU cc_start: 0.9106 (mt) cc_final: 0.8893 (mt) REVERT: 3 384 MET cc_start: 0.8471 (tmm) cc_final: 0.8119 (tmm) REVERT: 3 454 GLU cc_start: 0.8775 (tp30) cc_final: 0.8494 (tm-30) REVERT: 3 543 PHE cc_start: 0.7694 (m-80) cc_final: 0.7189 (m-80) REVERT: 3 551 ASP cc_start: 0.6889 (t70) cc_final: 0.6225 (m-30) REVERT: 4 272 MET cc_start: 0.9442 (mmp) cc_final: 0.9137 (ptt) REVERT: 4 554 LYS cc_start: 0.7417 (mttt) cc_final: 0.6905 (tptt) REVERT: 4 578 LEU cc_start: 0.9616 (mp) cc_final: 0.9323 (mm) REVERT: 4 637 MET cc_start: 0.2855 (tpt) cc_final: 0.1690 (mmm) REVERT: 4 651 GLN cc_start: 0.8687 (mt0) cc_final: 0.8035 (mp10) REVERT: 4 801 MET cc_start: 0.9038 (ttm) cc_final: 0.8740 (mtp) REVERT: 4 902 ASP cc_start: 0.9203 (m-30) cc_final: 0.8654 (p0) REVERT: 4 903 ILE cc_start: 0.8415 (mt) cc_final: 0.7976 (mm) REVERT: 5 41 ASP cc_start: 0.9580 (m-30) cc_final: 0.8996 (t0) REVERT: 5 67 HIS cc_start: 0.9337 (m90) cc_final: 0.9083 (m-70) REVERT: 5 252 ASP cc_start: 0.8286 (t0) cc_final: 0.7711 (t0) REVERT: 5 362 ARG cc_start: 0.9304 (mtt180) cc_final: 0.8944 (mtt180) REVERT: 5 393 MET cc_start: 0.8355 (mmp) cc_final: 0.7904 (mmm) REVERT: 5 509 ILE cc_start: 0.9393 (pt) cc_final: 0.9131 (tp) REVERT: 5 511 THR cc_start: 0.8255 (p) cc_final: 0.7907 (p) REVERT: 5 520 LEU cc_start: 0.9003 (tt) cc_final: 0.8553 (mt) REVERT: 5 552 MET cc_start: 0.8737 (mmm) cc_final: 0.8211 (mmm) REVERT: 5 576 HIS cc_start: 0.8989 (m90) cc_final: 0.8585 (m90) REVERT: 6 378 ASP cc_start: 0.9410 (p0) cc_final: 0.8658 (t0) REVERT: 6 384 ASP cc_start: 0.9531 (t0) cc_final: 0.8666 (p0) REVERT: 6 519 MET cc_start: 0.9472 (mtt) cc_final: 0.8818 (mtp) REVERT: 6 551 MET cc_start: 0.8938 (mtp) cc_final: 0.8500 (tpt) REVERT: 6 629 MET cc_start: 0.6879 (ttp) cc_final: 0.6447 (tpp) REVERT: 6 661 ILE cc_start: 0.9280 (mt) cc_final: 0.8896 (tt) REVERT: 6 699 LEU cc_start: 0.8887 (mp) cc_final: 0.8601 (mt) REVERT: 6 720 ASN cc_start: 0.9520 (t0) cc_final: 0.9020 (m110) REVERT: 6 735 HIS cc_start: 0.8300 (m-70) cc_final: 0.7937 (m90) REVERT: 6 803 MET cc_start: 0.8994 (mmp) cc_final: 0.8611 (mmm) REVERT: 6 915 MET cc_start: 0.7619 (mmp) cc_final: 0.7307 (mmt) REVERT: 7 29 LYS cc_start: 0.6873 (tptt) cc_final: 0.6438 (tppt) REVERT: 7 376 LEU cc_start: 0.9638 (tp) cc_final: 0.9384 (tp) REVERT: 7 457 CYS cc_start: 0.6454 (t) cc_final: 0.5715 (t) REVERT: 7 459 MET cc_start: 0.9001 (mmp) cc_final: 0.8638 (mmm) REVERT: A 164 ASP cc_start: 0.9727 (m-30) cc_final: 0.9387 (t0) REVERT: B 20 VAL cc_start: 0.9868 (m) cc_final: 0.9652 (p) REVERT: B 134 PHE cc_start: 0.8518 (m-80) cc_final: 0.8156 (m-80) REVERT: B 147 ASP cc_start: 0.9562 (p0) cc_final: 0.9184 (p0) REVERT: B 150 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9231 (mt-10) REVERT: B 161 LYS cc_start: 0.8846 (mptt) cc_final: 0.8595 (mmmt) REVERT: B 189 MET cc_start: 0.9617 (mmp) cc_final: 0.9298 (mmm) REVERT: B 190 ASP cc_start: 0.9359 (t70) cc_final: 0.8955 (m-30) REVERT: C 104 PHE cc_start: 0.9415 (t80) cc_final: 0.9190 (t80) REVERT: C 126 GLU cc_start: 0.9740 (tp30) cc_final: 0.9512 (tm-30) REVERT: C 134 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9114 (tm-30) REVERT: C 172 MET cc_start: 0.9280 (tmm) cc_final: 0.8925 (tmm) REVERT: C 175 GLU cc_start: 0.9810 (tp30) cc_final: 0.9564 (pp20) REVERT: C 176 ILE cc_start: 0.9706 (pt) cc_final: 0.9443 (pt) REVERT: D 68 LYS cc_start: 0.9693 (ptpp) cc_final: 0.9440 (ptmm) REVERT: D 84 MET cc_start: 0.9130 (tmm) cc_final: 0.8837 (tmm) REVERT: D 93 MET cc_start: 0.9808 (mmp) cc_final: 0.9284 (mmm) REVERT: D 220 ASP cc_start: 0.9602 (m-30) cc_final: 0.9140 (m-30) REVERT: D 277 MET cc_start: 0.9004 (mtt) cc_final: 0.8804 (mmt) REVERT: E 40 CYS cc_start: 0.9216 (m) cc_final: 0.8624 (p) REVERT: E 44 MET cc_start: 0.9781 (ptt) cc_final: 0.9578 (ptp) REVERT: E 362 MET cc_start: 0.9492 (tpt) cc_final: 0.8462 (tpt) REVERT: E 366 MET cc_start: 0.9385 (mtt) cc_final: 0.9037 (mmt) REVERT: E 380 MET cc_start: 0.9068 (mmp) cc_final: 0.8493 (mmm) REVERT: E 387 GLU cc_start: 0.9792 (mm-30) cc_final: 0.9558 (tp30) REVERT: E 407 ASP cc_start: 0.9123 (m-30) cc_final: 0.8131 (t0) REVERT: E 482 ASP cc_start: 0.9574 (t0) cc_final: 0.9364 (t0) REVERT: E 537 ASP cc_start: 0.9265 (m-30) cc_final: 0.8678 (p0) REVERT: E 538 LEU cc_start: 0.8983 (mt) cc_final: 0.8771 (mt) outliers start: 2 outliers final: 2 residues processed: 418 average time/residue: 0.5010 time to fit residues: 348.2103 Evaluate side-chains 319 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 time to evaluate : 4.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 164 optimal weight: 30.0000 chunk 440 optimal weight: 4.9990 chunk 96 optimal weight: 0.0970 chunk 287 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 489 optimal weight: 0.8980 chunk 406 optimal weight: 0.0470 chunk 226 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN 4 889 GLN ** 5 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 41467 Z= 0.196 Angle : 0.810 17.606 56108 Z= 0.414 Chirality : 0.046 0.396 6492 Planarity : 0.004 0.055 7133 Dihedral : 9.560 171.542 5773 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.80 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.07 % Favored : 90.05 % Rotamer: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.89 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4995 helix: -0.60 (0.11), residues: 1898 sheet: -2.07 (0.19), residues: 584 loop : -1.48 (0.13), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 74 HIS 0.009 0.001 HIS B 6 PHE 0.016 0.001 PHE 3 421 TYR 0.021 0.001 TYR 6 828 ARG 0.011 0.000 ARG 4 909 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 267 MET cc_start: 0.9270 (ptp) cc_final: 0.9043 (ptt) REVERT: 2 598 LEU cc_start: 0.9429 (mp) cc_final: 0.9089 (mt) REVERT: 2 609 PHE cc_start: 0.8169 (m-80) cc_final: 0.7473 (m-80) REVERT: 2 626 GLN cc_start: 0.8401 (pt0) cc_final: 0.7830 (tm-30) REVERT: 2 640 LEU cc_start: 0.8859 (tp) cc_final: 0.8636 (tt) REVERT: 2 677 PHE cc_start: 0.9046 (m-80) cc_final: 0.8673 (m-80) REVERT: 2 823 MET cc_start: 0.9249 (ptp) cc_final: 0.8717 (ptp) REVERT: 3 136 MET cc_start: 0.9354 (mmm) cc_final: 0.9017 (mmm) REVERT: 3 179 LEU cc_start: 0.9412 (tp) cc_final: 0.9161 (tp) REVERT: 3 183 GLU cc_start: 0.9132 (pm20) cc_final: 0.8290 (mm-30) REVERT: 3 252 ASP cc_start: 0.8694 (t0) cc_final: 0.7592 (p0) REVERT: 3 367 LEU cc_start: 0.9094 (mt) cc_final: 0.8884 (mt) REVERT: 3 384 MET cc_start: 0.8433 (tmm) cc_final: 0.8102 (tmm) REVERT: 3 454 GLU cc_start: 0.8754 (tp30) cc_final: 0.8472 (tm-30) REVERT: 3 551 ASP cc_start: 0.6650 (t70) cc_final: 0.6157 (m-30) REVERT: 4 272 MET cc_start: 0.9450 (mmp) cc_final: 0.9177 (ptt) REVERT: 4 328 LEU cc_start: 0.9407 (mt) cc_final: 0.9135 (mt) REVERT: 4 554 LYS cc_start: 0.7289 (mttt) cc_final: 0.6762 (tptt) REVERT: 4 637 MET cc_start: 0.2604 (tpt) cc_final: 0.2035 (mmm) REVERT: 4 651 GLN cc_start: 0.8606 (mt0) cc_final: 0.8071 (mp10) REVERT: 4 682 TYR cc_start: 0.8304 (p90) cc_final: 0.8089 (p90) REVERT: 4 801 MET cc_start: 0.9151 (ttm) cc_final: 0.8714 (mtp) REVERT: 4 902 ASP cc_start: 0.9196 (m-30) cc_final: 0.8739 (p0) REVERT: 4 903 ILE cc_start: 0.8337 (mt) cc_final: 0.7976 (mm) REVERT: 5 252 ASP cc_start: 0.8339 (t0) cc_final: 0.7789 (t0) REVERT: 5 278 CYS cc_start: 0.6798 (m) cc_final: 0.6478 (m) REVERT: 5 393 MET cc_start: 0.8474 (mmp) cc_final: 0.7886 (mmt) REVERT: 5 509 ILE cc_start: 0.9322 (pt) cc_final: 0.9103 (tp) REVERT: 5 511 THR cc_start: 0.8291 (p) cc_final: 0.8025 (p) REVERT: 5 552 MET cc_start: 0.8673 (mmm) cc_final: 0.8080 (mmm) REVERT: 5 576 HIS cc_start: 0.9013 (m90) cc_final: 0.8520 (m-70) REVERT: 6 168 MET cc_start: 0.9680 (mmp) cc_final: 0.9476 (mmm) REVERT: 6 373 MET cc_start: 0.7999 (tmm) cc_final: 0.7786 (tmm) REVERT: 6 384 ASP cc_start: 0.9503 (t0) cc_final: 0.8591 (p0) REVERT: 6 519 MET cc_start: 0.9445 (mtt) cc_final: 0.8890 (mtp) REVERT: 6 551 MET cc_start: 0.8929 (mtp) cc_final: 0.8464 (tpt) REVERT: 6 661 ILE cc_start: 0.9196 (mt) cc_final: 0.8835 (tt) REVERT: 6 699 LEU cc_start: 0.8992 (mp) cc_final: 0.8484 (mp) REVERT: 6 720 ASN cc_start: 0.9548 (t0) cc_final: 0.9030 (m110) REVERT: 6 726 GLU cc_start: 0.9476 (tp30) cc_final: 0.9080 (tp30) REVERT: 6 735 HIS cc_start: 0.8291 (m-70) cc_final: 0.7909 (m90) REVERT: 6 803 MET cc_start: 0.9029 (mmp) cc_final: 0.8750 (mmm) REVERT: 7 29 LYS cc_start: 0.6899 (tptt) cc_final: 0.6513 (tppt) REVERT: 7 376 LEU cc_start: 0.9646 (tp) cc_final: 0.9421 (tp) REVERT: 7 457 CYS cc_start: 0.6443 (t) cc_final: 0.5218 (t) REVERT: A 79 MET cc_start: 0.9536 (mmm) cc_final: 0.9110 (mmm) REVERT: A 110 MET cc_start: 0.2899 (mmm) cc_final: 0.2667 (mmm) REVERT: A 164 ASP cc_start: 0.9744 (m-30) cc_final: 0.9348 (t0) REVERT: B 20 VAL cc_start: 0.9864 (m) cc_final: 0.9653 (p) REVERT: B 134 PHE cc_start: 0.8626 (m-80) cc_final: 0.8295 (m-80) REVERT: B 147 ASP cc_start: 0.9553 (p0) cc_final: 0.9155 (p0) REVERT: B 150 GLU cc_start: 0.9556 (mt-10) cc_final: 0.9229 (mt-10) REVERT: B 161 LYS cc_start: 0.8856 (mptt) cc_final: 0.8592 (mmmt) REVERT: B 189 MET cc_start: 0.9608 (mmp) cc_final: 0.9268 (mmm) REVERT: B 190 ASP cc_start: 0.9348 (t70) cc_final: 0.8951 (m-30) REVERT: C 104 PHE cc_start: 0.9374 (t80) cc_final: 0.9152 (t80) REVERT: C 109 ILE cc_start: 0.9732 (pt) cc_final: 0.9514 (mt) REVERT: C 134 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9186 (tm-30) REVERT: C 172 MET cc_start: 0.9257 (tmm) cc_final: 0.8932 (tmm) REVERT: C 175 GLU cc_start: 0.9807 (tp30) cc_final: 0.9518 (pp20) REVERT: C 176 ILE cc_start: 0.9681 (pt) cc_final: 0.9446 (pt) REVERT: D 68 LYS cc_start: 0.9704 (ptpp) cc_final: 0.9451 (ptmm) REVERT: D 93 MET cc_start: 0.9797 (mmp) cc_final: 0.9277 (mmm) REVERT: D 220 ASP cc_start: 0.9529 (m-30) cc_final: 0.9295 (m-30) REVERT: E 40 CYS cc_start: 0.9192 (m) cc_final: 0.8732 (p) REVERT: E 362 MET cc_start: 0.9477 (tpt) cc_final: 0.8874 (tpt) REVERT: E 366 MET cc_start: 0.9400 (mtt) cc_final: 0.9080 (mmm) REVERT: E 380 MET cc_start: 0.9046 (mmt) cc_final: 0.8418 (mmm) REVERT: E 387 GLU cc_start: 0.9776 (mm-30) cc_final: 0.9543 (tp30) REVERT: E 407 ASP cc_start: 0.9102 (m-30) cc_final: 0.8161 (t0) REVERT: E 537 ASP cc_start: 0.9267 (m-30) cc_final: 0.8716 (p0) outliers start: 2 outliers final: 2 residues processed: 418 average time/residue: 0.4984 time to fit residues: 348.7813 Evaluate side-chains 322 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 5.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 472 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 278 optimal weight: 0.7980 chunk 357 optimal weight: 9.9990 chunk 277 optimal weight: 0.9990 chunk 412 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 487 optimal weight: 6.9990 chunk 305 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 225 optimal weight: 0.0570 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 551 GLN ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 425 ASN 7 538 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41467 Z= 0.194 Angle : 0.804 19.487 56108 Z= 0.411 Chirality : 0.046 0.402 6492 Planarity : 0.004 0.056 7133 Dihedral : 9.531 179.390 5773 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.03 % Favored : 90.05 % Rotamer: Outliers : 0.07 % Allowed : 1.98 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.89 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4995 helix: -0.45 (0.11), residues: 1911 sheet: -1.99 (0.19), residues: 576 loop : -1.43 (0.13), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 74 HIS 0.010 0.001 HIS B 6 PHE 0.019 0.001 PHE 7 355 TYR 0.022 0.001 TYR 6 689 ARG 0.006 0.000 ARG 4 909 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 415 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 598 LEU cc_start: 0.9418 (mp) cc_final: 0.9076 (mt) REVERT: 2 609 PHE cc_start: 0.8205 (m-80) cc_final: 0.7538 (m-80) REVERT: 2 626 GLN cc_start: 0.8362 (pt0) cc_final: 0.7791 (tm-30) REVERT: 2 640 LEU cc_start: 0.8879 (tp) cc_final: 0.8544 (tt) REVERT: 2 677 PHE cc_start: 0.9068 (m-80) cc_final: 0.8718 (m-80) REVERT: 3 136 MET cc_start: 0.9362 (mmm) cc_final: 0.9016 (mmm) REVERT: 3 179 LEU cc_start: 0.9433 (tp) cc_final: 0.9172 (tp) REVERT: 3 183 GLU cc_start: 0.9100 (pm20) cc_final: 0.8281 (mm-30) REVERT: 3 252 ASP cc_start: 0.8649 (t0) cc_final: 0.7712 (p0) REVERT: 3 384 MET cc_start: 0.8452 (tmm) cc_final: 0.8126 (tmm) REVERT: 3 406 LEU cc_start: 0.8804 (pp) cc_final: 0.8516 (pp) REVERT: 3 454 GLU cc_start: 0.8749 (tp30) cc_final: 0.8484 (tm-30) REVERT: 3 551 ASP cc_start: 0.6970 (t70) cc_final: 0.6457 (m-30) REVERT: 4 272 MET cc_start: 0.9386 (mmp) cc_final: 0.9089 (ptt) REVERT: 4 328 LEU cc_start: 0.9386 (mt) cc_final: 0.9101 (mt) REVERT: 4 637 MET cc_start: 0.2597 (tpt) cc_final: 0.1953 (mmm) REVERT: 4 651 GLN cc_start: 0.8624 (mt0) cc_final: 0.8068 (mp10) REVERT: 4 682 TYR cc_start: 0.8291 (p90) cc_final: 0.8075 (p90) REVERT: 4 801 MET cc_start: 0.9128 (ttm) cc_final: 0.8728 (mtp) REVERT: 4 834 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9243 (pptt) REVERT: 4 902 ASP cc_start: 0.9157 (m-30) cc_final: 0.8615 (p0) REVERT: 4 903 ILE cc_start: 0.8338 (mt) cc_final: 0.8010 (mm) REVERT: 5 41 ASP cc_start: 0.9581 (m-30) cc_final: 0.9146 (t0) REVERT: 5 252 ASP cc_start: 0.8329 (t0) cc_final: 0.7734 (t0) REVERT: 5 259 GLN cc_start: 0.9012 (tt0) cc_final: 0.8566 (tt0) REVERT: 5 393 MET cc_start: 0.8455 (mmp) cc_final: 0.7824 (mmt) REVERT: 5 485 MET cc_start: 0.5968 (ppp) cc_final: 0.5641 (ppp) REVERT: 5 509 ILE cc_start: 0.9362 (pt) cc_final: 0.9159 (tp) REVERT: 5 511 THR cc_start: 0.8312 (p) cc_final: 0.8056 (p) REVERT: 5 552 MET cc_start: 0.8609 (mmm) cc_final: 0.7998 (mmm) REVERT: 5 576 HIS cc_start: 0.8980 (m90) cc_final: 0.8587 (m-70) REVERT: 6 168 MET cc_start: 0.9682 (mmp) cc_final: 0.9468 (mmm) REVERT: 6 373 MET cc_start: 0.8023 (tmm) cc_final: 0.7813 (tmm) REVERT: 6 384 ASP cc_start: 0.9497 (t0) cc_final: 0.8598 (p0) REVERT: 6 519 MET cc_start: 0.9430 (mtt) cc_final: 0.8777 (mtp) REVERT: 6 551 MET cc_start: 0.8962 (mtp) cc_final: 0.8599 (mmm) REVERT: 6 661 ILE cc_start: 0.9246 (mt) cc_final: 0.8854 (tt) REVERT: 6 699 LEU cc_start: 0.8935 (mp) cc_final: 0.8310 (mp) REVERT: 6 726 GLU cc_start: 0.9471 (tp30) cc_final: 0.9081 (tp30) REVERT: 6 803 MET cc_start: 0.9013 (mmp) cc_final: 0.8740 (mmm) REVERT: 7 29 LYS cc_start: 0.6902 (tptt) cc_final: 0.6519 (tppt) REVERT: 7 66 MET cc_start: 0.8940 (mmp) cc_final: 0.8272 (ptt) REVERT: 7 376 LEU cc_start: 0.9652 (tp) cc_final: 0.9428 (tp) REVERT: A 15 ARG cc_start: 0.9539 (ttt180) cc_final: 0.9182 (ptm-80) REVERT: A 38 ARG cc_start: 0.9357 (mmp80) cc_final: 0.9155 (mmm160) REVERT: A 79 MET cc_start: 0.9567 (mmm) cc_final: 0.9155 (mmm) REVERT: A 164 ASP cc_start: 0.9751 (m-30) cc_final: 0.9334 (t0) REVERT: B 20 VAL cc_start: 0.9879 (m) cc_final: 0.9654 (p) REVERT: B 134 PHE cc_start: 0.8600 (m-80) cc_final: 0.8213 (m-80) REVERT: B 147 ASP cc_start: 0.9548 (p0) cc_final: 0.9126 (p0) REVERT: B 189 MET cc_start: 0.9621 (mmp) cc_final: 0.9262 (mmm) REVERT: B 190 ASP cc_start: 0.9341 (t70) cc_final: 0.8967 (m-30) REVERT: C 104 PHE cc_start: 0.9376 (t80) cc_final: 0.9145 (t80) REVERT: C 109 ILE cc_start: 0.9706 (pt) cc_final: 0.9483 (mt) REVERT: C 124 VAL cc_start: 0.9801 (t) cc_final: 0.9537 (p) REVERT: C 134 GLU cc_start: 0.9471 (tm-30) cc_final: 0.8954 (tm-30) REVERT: C 172 MET cc_start: 0.9313 (tmm) cc_final: 0.8929 (tmm) REVERT: C 175 GLU cc_start: 0.9778 (tp30) cc_final: 0.9511 (pp20) REVERT: D 64 MET cc_start: 0.9785 (tpp) cc_final: 0.9219 (tpp) REVERT: D 68 LYS cc_start: 0.9705 (ptpp) cc_final: 0.9376 (pttm) REVERT: D 93 MET cc_start: 0.9781 (mmp) cc_final: 0.9243 (mmm) REVERT: D 129 MET cc_start: 0.9288 (mmt) cc_final: 0.9030 (mmt) REVERT: D 220 ASP cc_start: 0.9497 (m-30) cc_final: 0.9221 (m-30) REVERT: E 40 CYS cc_start: 0.9207 (m) cc_final: 0.8753 (p) REVERT: E 366 MET cc_start: 0.9398 (mtt) cc_final: 0.9016 (mtt) REVERT: E 380 MET cc_start: 0.9052 (mmt) cc_final: 0.8397 (mmm) REVERT: E 387 GLU cc_start: 0.9735 (mm-30) cc_final: 0.9504 (tp30) REVERT: E 407 ASP cc_start: 0.9139 (m-30) cc_final: 0.8123 (t0) REVERT: E 537 ASP cc_start: 0.9342 (m-30) cc_final: 0.8768 (p0) outliers start: 3 outliers final: 2 residues processed: 418 average time/residue: 0.5075 time to fit residues: 354.0503 Evaluate side-chains 315 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 313 time to evaluate : 4.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 301 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 383 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 579 GLN ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 ASN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41467 Z= 0.216 Angle : 0.808 20.025 56108 Z= 0.415 Chirality : 0.046 0.397 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.407 169.936 5773 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 27.24 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.31 % Favored : 89.77 % Rotamer: Outliers : 0.07 % Allowed : 1.11 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.92 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.12), residues: 4995 helix: -0.32 (0.12), residues: 1907 sheet: -1.92 (0.20), residues: 572 loop : -1.48 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 74 HIS 0.009 0.001 HIS B 6 PHE 0.018 0.001 PHE 3 520 TYR 0.018 0.001 TYR 6 828 ARG 0.012 0.000 ARG 4 909 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 394 time to evaluate : 5.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 598 LEU cc_start: 0.9493 (mp) cc_final: 0.9090 (mt) REVERT: 2 609 PHE cc_start: 0.8055 (m-80) cc_final: 0.7429 (m-80) REVERT: 2 626 GLN cc_start: 0.8396 (pt0) cc_final: 0.7857 (tm-30) REVERT: 2 677 PHE cc_start: 0.9151 (m-80) cc_final: 0.8780 (m-80) REVERT: 3 136 MET cc_start: 0.9378 (mmm) cc_final: 0.9036 (mmm) REVERT: 3 179 LEU cc_start: 0.9429 (tp) cc_final: 0.9151 (tp) REVERT: 3 183 GLU cc_start: 0.9109 (pm20) cc_final: 0.8882 (pm20) REVERT: 3 252 ASP cc_start: 0.8729 (t0) cc_final: 0.8459 (t0) REVERT: 3 367 LEU cc_start: 0.9064 (mt) cc_final: 0.8845 (mt) REVERT: 3 384 MET cc_start: 0.8489 (tmm) cc_final: 0.8167 (tmm) REVERT: 3 454 GLU cc_start: 0.8790 (tp30) cc_final: 0.8551 (tm-30) REVERT: 3 551 ASP cc_start: 0.7011 (t70) cc_final: 0.6428 (m-30) REVERT: 4 272 MET cc_start: 0.9397 (mmp) cc_final: 0.9033 (ptt) REVERT: 4 328 LEU cc_start: 0.9390 (mt) cc_final: 0.9097 (mt) REVERT: 4 554 LYS cc_start: 0.7362 (tttt) cc_final: 0.6915 (tptp) REVERT: 4 651 GLN cc_start: 0.8626 (mt0) cc_final: 0.8113 (mp10) REVERT: 4 682 TYR cc_start: 0.8317 (p90) cc_final: 0.8098 (p90) REVERT: 4 801 MET cc_start: 0.9176 (ttm) cc_final: 0.8741 (mtp) REVERT: 4 902 ASP cc_start: 0.9169 (m-30) cc_final: 0.8710 (p0) REVERT: 4 903 ILE cc_start: 0.8312 (mt) cc_final: 0.7992 (mm) REVERT: 5 41 ASP cc_start: 0.9569 (m-30) cc_final: 0.9059 (t0) REVERT: 5 252 ASP cc_start: 0.8397 (t0) cc_final: 0.7817 (t0) REVERT: 5 278 CYS cc_start: 0.6657 (m) cc_final: 0.6239 (m) REVERT: 5 393 MET cc_start: 0.8296 (mmp) cc_final: 0.7738 (mmt) REVERT: 5 485 MET cc_start: 0.6142 (ppp) cc_final: 0.5838 (ppp) REVERT: 5 511 THR cc_start: 0.8306 (p) cc_final: 0.8095 (p) REVERT: 5 552 MET cc_start: 0.8648 (mmm) cc_final: 0.8062 (mmm) REVERT: 5 576 HIS cc_start: 0.8942 (m90) cc_final: 0.8573 (m-70) REVERT: 6 168 MET cc_start: 0.9673 (mmp) cc_final: 0.9462 (mmm) REVERT: 6 373 MET cc_start: 0.8062 (tmm) cc_final: 0.7858 (tmm) REVERT: 6 384 ASP cc_start: 0.9531 (t0) cc_final: 0.8659 (p0) REVERT: 6 519 MET cc_start: 0.9444 (mtt) cc_final: 0.8881 (mtp) REVERT: 6 551 MET cc_start: 0.8991 (mtp) cc_final: 0.8424 (tpt) REVERT: 6 699 LEU cc_start: 0.8894 (mp) cc_final: 0.8341 (mp) REVERT: 6 726 GLU cc_start: 0.9483 (tp30) cc_final: 0.9086 (tp30) REVERT: 6 803 MET cc_start: 0.9021 (mmp) cc_final: 0.8723 (mmm) REVERT: 7 29 LYS cc_start: 0.6772 (tptt) cc_final: 0.6352 (tppt) REVERT: 7 376 LEU cc_start: 0.9635 (tp) cc_final: 0.9408 (tp) REVERT: A 15 ARG cc_start: 0.9542 (ttt180) cc_final: 0.9194 (ptm-80) REVERT: A 79 MET cc_start: 0.9640 (mmm) cc_final: 0.9244 (mmm) REVERT: A 164 ASP cc_start: 0.9743 (m-30) cc_final: 0.9478 (t0) REVERT: B 20 VAL cc_start: 0.9873 (m) cc_final: 0.9643 (p) REVERT: B 134 PHE cc_start: 0.8580 (m-80) cc_final: 0.8183 (m-80) REVERT: B 189 MET cc_start: 0.9600 (mmp) cc_final: 0.9288 (mmm) REVERT: B 190 ASP cc_start: 0.9374 (t70) cc_final: 0.8990 (m-30) REVERT: C 3 TYR cc_start: 0.8396 (t80) cc_final: 0.7306 (t80) REVERT: C 8 ASP cc_start: 0.9469 (m-30) cc_final: 0.9162 (m-30) REVERT: C 104 PHE cc_start: 0.9372 (t80) cc_final: 0.9088 (t80) REVERT: C 124 VAL cc_start: 0.9823 (t) cc_final: 0.9560 (p) REVERT: C 134 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9055 (tm-30) REVERT: C 172 MET cc_start: 0.9341 (tmm) cc_final: 0.8946 (tmm) REVERT: C 175 GLU cc_start: 0.9782 (tp30) cc_final: 0.9574 (pp20) REVERT: C 176 ILE cc_start: 0.9705 (pt) cc_final: 0.9476 (pt) REVERT: D 64 MET cc_start: 0.9789 (tpp) cc_final: 0.9066 (tpp) REVERT: D 68 LYS cc_start: 0.9706 (ptpp) cc_final: 0.9461 (ptpp) REVERT: D 93 MET cc_start: 0.9761 (mmp) cc_final: 0.9217 (mmm) REVERT: D 220 ASP cc_start: 0.9435 (m-30) cc_final: 0.9108 (m-30) REVERT: E 40 CYS cc_start: 0.9222 (m) cc_final: 0.8750 (p) REVERT: E 366 MET cc_start: 0.9380 (mtt) cc_final: 0.9067 (mmt) REVERT: E 380 MET cc_start: 0.9058 (mmt) cc_final: 0.8427 (mmm) REVERT: E 387 GLU cc_start: 0.9734 (mm-30) cc_final: 0.9466 (tp30) REVERT: E 407 ASP cc_start: 0.9213 (m-30) cc_final: 0.8343 (t0) REVERT: E 537 ASP cc_start: 0.9299 (m-30) cc_final: 0.8711 (p0) REVERT: E 538 LEU cc_start: 0.8922 (mt) cc_final: 0.8699 (mt) outliers start: 3 outliers final: 2 residues processed: 397 average time/residue: 0.5152 time to fit residues: 340.7595 Evaluate side-chains 307 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 4.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 443 optimal weight: 8.9990 chunk 467 optimal weight: 8.9990 chunk 426 optimal weight: 4.9990 chunk 454 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 410 optimal weight: 3.9990 chunk 429 optimal weight: 3.9990 chunk 452 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 871 ASN 4 889 GLN ** 5 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS A 50 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41467 Z= 0.218 Angle : 0.806 20.608 56108 Z= 0.414 Chirality : 0.046 0.419 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.322 160.865 5773 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.23 % Favored : 89.77 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.92 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.63 (0.12), residues: 4995 helix: -0.26 (0.12), residues: 1898 sheet: -1.89 (0.20), residues: 553 loop : -1.51 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 74 HIS 0.009 0.001 HIS B 6 PHE 0.019 0.001 PHE C 192 TYR 0.015 0.001 TYR 6 689 ARG 0.009 0.000 ARG 4 909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 5.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 2 598 LEU cc_start: 0.9531 (mp) cc_final: 0.9164 (mt) REVERT: 2 626 GLN cc_start: 0.8383 (pt0) cc_final: 0.7862 (tm-30) REVERT: 2 677 PHE cc_start: 0.9183 (m-80) cc_final: 0.8835 (m-80) REVERT: 3 136 MET cc_start: 0.9409 (mmm) cc_final: 0.9034 (mmm) REVERT: 3 179 LEU cc_start: 0.9396 (tp) cc_final: 0.9117 (tp) REVERT: 3 252 ASP cc_start: 0.8732 (t0) cc_final: 0.8457 (t0) REVERT: 3 384 MET cc_start: 0.8475 (tmm) cc_final: 0.8165 (tmm) REVERT: 3 471 CYS cc_start: 0.7388 (m) cc_final: 0.7124 (m) REVERT: 3 478 MET cc_start: 0.6450 (tpp) cc_final: 0.6039 (tmm) REVERT: 3 551 ASP cc_start: 0.7067 (t70) cc_final: 0.6446 (m-30) REVERT: 4 272 MET cc_start: 0.9331 (mmp) cc_final: 0.8950 (ptt) REVERT: 4 317 LEU cc_start: 0.9333 (tt) cc_final: 0.8899 (mt) REVERT: 4 328 LEU cc_start: 0.9403 (mt) cc_final: 0.9119 (mt) REVERT: 4 554 LYS cc_start: 0.7392 (tttt) cc_final: 0.6964 (tptp) REVERT: 4 637 MET cc_start: 0.3005 (mmm) cc_final: 0.0553 (tpp) REVERT: 4 651 GLN cc_start: 0.8637 (mt0) cc_final: 0.8164 (mp10) REVERT: 4 801 MET cc_start: 0.9211 (ttm) cc_final: 0.8772 (mtp) REVERT: 4 834 LYS cc_start: 0.9579 (mmtt) cc_final: 0.9334 (pptt) REVERT: 4 902 ASP cc_start: 0.9171 (m-30) cc_final: 0.8703 (p0) REVERT: 4 903 ILE cc_start: 0.8302 (mt) cc_final: 0.7984 (mm) REVERT: 5 41 ASP cc_start: 0.9517 (m-30) cc_final: 0.9003 (t0) REVERT: 5 252 ASP cc_start: 0.8471 (t0) cc_final: 0.7918 (t0) REVERT: 5 393 MET cc_start: 0.8305 (mmp) cc_final: 0.7659 (mmm) REVERT: 5 520 LEU cc_start: 0.8949 (tt) cc_final: 0.8557 (mt) REVERT: 5 552 MET cc_start: 0.8558 (mmm) cc_final: 0.7967 (mmm) REVERT: 5 576 HIS cc_start: 0.8991 (m90) cc_final: 0.8532 (m-70) REVERT: 5 599 MET cc_start: 0.9311 (tpp) cc_final: 0.8990 (mtp) REVERT: 5 689 MET cc_start: 0.9146 (tmm) cc_final: 0.8801 (tpt) REVERT: 6 168 MET cc_start: 0.9651 (mmp) cc_final: 0.9444 (mmm) REVERT: 6 384 ASP cc_start: 0.9578 (t0) cc_final: 0.8739 (p0) REVERT: 6 519 MET cc_start: 0.9436 (mtt) cc_final: 0.8860 (mtp) REVERT: 6 551 MET cc_start: 0.9024 (mtp) cc_final: 0.8472 (tpt) REVERT: 6 669 HIS cc_start: 0.8243 (t-90) cc_final: 0.7930 (t70) REVERT: 6 699 LEU cc_start: 0.8905 (mp) cc_final: 0.8445 (mp) REVERT: 6 714 VAL cc_start: 0.8933 (t) cc_final: 0.8619 (p) REVERT: 6 726 GLU cc_start: 0.9459 (tp30) cc_final: 0.9073 (tp30) REVERT: 6 730 HIS cc_start: 0.8637 (t-90) cc_final: 0.8431 (t-90) REVERT: 6 735 HIS cc_start: 0.8507 (m-70) cc_final: 0.8154 (m90) REVERT: 6 794 ARG cc_start: 0.6722 (mmt180) cc_final: 0.2888 (ttt180) REVERT: 6 803 MET cc_start: 0.8931 (mmp) cc_final: 0.8638 (mmm) REVERT: 7 29 LYS cc_start: 0.6711 (tptt) cc_final: 0.6305 (tppt) REVERT: 7 376 LEU cc_start: 0.9653 (tp) cc_final: 0.9433 (tp) REVERT: 7 459 MET cc_start: 0.9040 (mmp) cc_final: 0.8771 (mmm) REVERT: A 15 ARG cc_start: 0.9571 (ttt180) cc_final: 0.9218 (ptm-80) REVERT: A 79 MET cc_start: 0.9649 (mmm) cc_final: 0.9261 (mmm) REVERT: A 110 MET cc_start: 0.2389 (mmm) cc_final: 0.2104 (mmm) REVERT: A 164 ASP cc_start: 0.9759 (m-30) cc_final: 0.9469 (t0) REVERT: B 20 VAL cc_start: 0.9872 (m) cc_final: 0.9634 (p) REVERT: B 134 PHE cc_start: 0.8579 (m-80) cc_final: 0.8193 (m-80) REVERT: B 189 MET cc_start: 0.9596 (mmp) cc_final: 0.9251 (mmm) REVERT: B 190 ASP cc_start: 0.9366 (t70) cc_final: 0.8999 (m-30) REVERT: C 3 TYR cc_start: 0.8391 (t80) cc_final: 0.7201 (t80) REVERT: C 8 ASP cc_start: 0.9454 (m-30) cc_final: 0.9199 (m-30) REVERT: C 104 PHE cc_start: 0.9378 (t80) cc_final: 0.9131 (t80) REVERT: C 109 ILE cc_start: 0.9740 (pt) cc_final: 0.9527 (mt) REVERT: C 134 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9057 (tm-30) REVERT: C 172 MET cc_start: 0.9348 (tmm) cc_final: 0.8966 (tmm) REVERT: C 175 GLU cc_start: 0.9796 (tp30) cc_final: 0.9568 (pp20) REVERT: C 176 ILE cc_start: 0.9699 (pt) cc_final: 0.9451 (pt) REVERT: D 64 MET cc_start: 0.9789 (tpp) cc_final: 0.9042 (tpp) REVERT: D 68 LYS cc_start: 0.9700 (ptpp) cc_final: 0.9437 (ptpp) REVERT: D 93 MET cc_start: 0.9761 (mmp) cc_final: 0.9235 (mmm) REVERT: D 220 ASP cc_start: 0.9460 (m-30) cc_final: 0.9052 (m-30) REVERT: D 277 MET cc_start: 0.8339 (mmt) cc_final: 0.7808 (mmp) REVERT: E 40 CYS cc_start: 0.9231 (m) cc_final: 0.8766 (p) REVERT: E 44 MET cc_start: 0.9745 (ptp) cc_final: 0.9496 (ptt) REVERT: E 366 MET cc_start: 0.9423 (mtt) cc_final: 0.9078 (mmt) REVERT: E 380 MET cc_start: 0.9042 (mmt) cc_final: 0.8441 (mmm) REVERT: E 387 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9469 (tp30) REVERT: E 407 ASP cc_start: 0.9215 (m-30) cc_final: 0.8450 (t0) REVERT: E 537 ASP cc_start: 0.9314 (m-30) cc_final: 0.8740 (p0) outliers start: 3 outliers final: 2 residues processed: 394 average time/residue: 0.5135 time to fit residues: 341.2114 Evaluate side-chains 312 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 310 time to evaluate : 5.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 298 optimal weight: 6.9990 chunk 480 optimal weight: 0.4980 chunk 293 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 504 optimal weight: 3.9990 chunk 463 optimal weight: 9.9990 chunk 401 optimal weight: 0.0670 chunk 41 optimal weight: 20.0000 chunk 310 optimal weight: 0.7980 chunk 246 optimal weight: 4.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 889 GLN 5 64 ASN 5 67 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 326 HIS 7 538 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41467 Z= 0.186 Angle : 0.800 20.795 56108 Z= 0.407 Chirality : 0.046 0.387 6492 Planarity : 0.004 0.060 7133 Dihedral : 9.174 157.939 5773 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 1.02 % Allowed : 9.01 % Favored : 89.97 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4995 helix: -0.15 (0.12), residues: 1909 sheet: -1.75 (0.21), residues: 544 loop : -1.44 (0.13), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 74 HIS 0.010 0.001 HIS B 6 PHE 0.026 0.001 PHE C 192 TYR 0.014 0.001 TYR 6 174 ARG 0.009 0.000 ARG E 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 410 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 2 598 LEU cc_start: 0.9504 (mp) cc_final: 0.9142 (mt) REVERT: 2 624 MET cc_start: 0.8522 (pmm) cc_final: 0.8294 (pmm) REVERT: 2 626 GLN cc_start: 0.8110 (pt0) cc_final: 0.7497 (tm-30) REVERT: 2 677 PHE cc_start: 0.9161 (m-80) cc_final: 0.8833 (m-80) REVERT: 3 136 MET cc_start: 0.9346 (mmm) cc_final: 0.9028 (mmm) REVERT: 3 179 LEU cc_start: 0.9349 (tp) cc_final: 0.9068 (tp) REVERT: 3 252 ASP cc_start: 0.8647 (t0) cc_final: 0.8280 (t0) REVERT: 3 384 MET cc_start: 0.8407 (tmm) cc_final: 0.8162 (tmm) REVERT: 3 471 CYS cc_start: 0.7327 (m) cc_final: 0.6943 (m) REVERT: 3 489 VAL cc_start: 0.9428 (t) cc_final: 0.9172 (p) REVERT: 3 551 ASP cc_start: 0.7006 (t70) cc_final: 0.6418 (m-30) REVERT: 4 272 MET cc_start: 0.9384 (mmp) cc_final: 0.9030 (ptt) REVERT: 4 317 LEU cc_start: 0.9304 (tt) cc_final: 0.8863 (mt) REVERT: 4 382 MET cc_start: 0.8257 (ptp) cc_final: 0.8051 (ptp) REVERT: 4 554 LYS cc_start: 0.7304 (tttt) cc_final: 0.6998 (tmtt) REVERT: 4 637 MET cc_start: 0.3097 (mmm) cc_final: 0.2427 (tpp) REVERT: 4 649 MET cc_start: 0.8042 (ttp) cc_final: 0.7783 (tmm) REVERT: 4 651 GLN cc_start: 0.8588 (mt0) cc_final: 0.8157 (mp10) REVERT: 4 801 MET cc_start: 0.9201 (ttm) cc_final: 0.8878 (mtp) REVERT: 4 834 LYS cc_start: 0.9561 (mmtt) cc_final: 0.9318 (pptt) REVERT: 5 41 ASP cc_start: 0.9517 (m-30) cc_final: 0.9012 (t0) REVERT: 5 252 ASP cc_start: 0.8476 (t0) cc_final: 0.7934 (t0) REVERT: 5 278 CYS cc_start: 0.6262 (m) cc_final: 0.6035 (m) REVERT: 5 356 GLU cc_start: 0.8999 (pt0) cc_final: 0.8720 (pt0) REVERT: 5 393 MET cc_start: 0.8246 (mmp) cc_final: 0.7775 (mmm) REVERT: 5 485 MET cc_start: 0.6184 (ppp) cc_final: 0.5751 (ppp) REVERT: 5 520 LEU cc_start: 0.9029 (tt) cc_final: 0.8510 (mt) REVERT: 5 552 MET cc_start: 0.8612 (mmm) cc_final: 0.8095 (mmm) REVERT: 5 576 HIS cc_start: 0.8940 (m90) cc_final: 0.8490 (m-70) REVERT: 5 599 MET cc_start: 0.9332 (tpp) cc_final: 0.9055 (mtp) REVERT: 5 689 MET cc_start: 0.9057 (tmm) cc_final: 0.8758 (tpt) REVERT: 6 168 MET cc_start: 0.9654 (mmp) cc_final: 0.9443 (mmp) REVERT: 6 373 MET cc_start: 0.8124 (tmm) cc_final: 0.7819 (tmm) REVERT: 6 384 ASP cc_start: 0.9503 (t0) cc_final: 0.8613 (p0) REVERT: 6 519 MET cc_start: 0.9429 (mtt) cc_final: 0.8890 (mtp) REVERT: 6 699 LEU cc_start: 0.8785 (mp) cc_final: 0.8334 (mp) REVERT: 6 714 VAL cc_start: 0.8805 (t) cc_final: 0.8529 (p) REVERT: 6 726 GLU cc_start: 0.9426 (tp30) cc_final: 0.9058 (tp30) REVERT: 6 794 ARG cc_start: 0.6453 (mmt180) cc_final: 0.2594 (tpt-90) REVERT: 7 29 LYS cc_start: 0.6879 (tptt) cc_final: 0.6520 (tppt) REVERT: 7 313 CYS cc_start: 0.9055 (m) cc_final: 0.8830 (p) REVERT: 7 376 LEU cc_start: 0.9653 (tp) cc_final: 0.9399 (tp) REVERT: 7 435 LEU cc_start: 0.9190 (mm) cc_final: 0.8911 (mm) REVERT: A 38 ARG cc_start: 0.9415 (mmp80) cc_final: 0.9175 (mmm160) REVERT: A 79 MET cc_start: 0.9645 (mmm) cc_final: 0.9323 (mmp) REVERT: A 110 MET cc_start: 0.2338 (mmm) cc_final: 0.2067 (mmm) REVERT: A 164 ASP cc_start: 0.9771 (m-30) cc_final: 0.9400 (t0) REVERT: B 134 PHE cc_start: 0.8514 (m-80) cc_final: 0.8137 (m-80) REVERT: B 189 MET cc_start: 0.9568 (mmp) cc_final: 0.9269 (mmm) REVERT: B 190 ASP cc_start: 0.9326 (t70) cc_final: 0.8996 (m-30) REVERT: C 3 TYR cc_start: 0.8151 (t80) cc_final: 0.7154 (t80) REVERT: C 8 ASP cc_start: 0.9523 (m-30) cc_final: 0.9170 (m-30) REVERT: C 134 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9243 (tm-30) REVERT: C 172 MET cc_start: 0.9345 (tmm) cc_final: 0.8940 (tmm) REVERT: C 175 GLU cc_start: 0.9794 (tp30) cc_final: 0.9556 (pp20) REVERT: C 176 ILE cc_start: 0.9696 (pt) cc_final: 0.9465 (pt) REVERT: D 93 MET cc_start: 0.9750 (mmp) cc_final: 0.9209 (mmm) REVERT: D 220 ASP cc_start: 0.9470 (m-30) cc_final: 0.9151 (m-30) REVERT: E 40 CYS cc_start: 0.9205 (m) cc_final: 0.8744 (p) REVERT: E 44 MET cc_start: 0.9716 (ptp) cc_final: 0.9470 (ptt) REVERT: E 366 MET cc_start: 0.9449 (mtt) cc_final: 0.9063 (mmt) REVERT: E 375 GLU cc_start: 0.9618 (pt0) cc_final: 0.9366 (pt0) REVERT: E 380 MET cc_start: 0.9050 (mmt) cc_final: 0.8793 (ttm) REVERT: E 387 GLU cc_start: 0.9709 (mm-30) cc_final: 0.9460 (tp30) REVERT: E 407 ASP cc_start: 0.9217 (m-30) cc_final: 0.8374 (t0) REVERT: E 537 ASP cc_start: 0.9392 (m-30) cc_final: 0.8821 (p0) outliers start: 3 outliers final: 2 residues processed: 413 average time/residue: 0.5074 time to fit residues: 352.0243 Evaluate side-chains 309 residues out of total 4555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 318 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 402 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 344 ASN ** 5 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.047316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.036459 restraints weight = 385319.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037598 restraints weight = 262387.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038473 restraints weight = 196724.528| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41467 Z= 0.218 Angle : 0.799 20.910 56108 Z= 0.410 Chirality : 0.046 0.405 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.124 161.743 5773 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 1.04 % Allowed : 9.41 % Favored : 89.55 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.89 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.46 (0.12), residues: 4995 helix: -0.07 (0.12), residues: 1899 sheet: -1.80 (0.21), residues: 530 loop : -1.46 (0.13), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 224 HIS 0.010 0.001 HIS 5 560 PHE 0.019 0.001 PHE 3 421 TYR 0.018 0.001 TYR 2 434 ARG 0.008 0.000 ARG 4 909 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8172.90 seconds wall clock time: 149 minutes 33.85 seconds (8973.85 seconds total)