Starting phenix.real_space_refine on Sun Nov 17 21:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8f_37353/11_2024/8w8f_37353_neut.cif" } resolution = 4.0 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= 0.008 sd= 0.070 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 29232 2.51 5 N 8143 2.21 5 O 8900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 46667 Number of models: 1 Model: "" Number of chains: 26 Chain: "a" Number of atoms: 4203 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 517, 4181 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 482} 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 Conformer: "B" Number of residues, atoms: 517, 4181 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 482} 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 bond proxies already assigned to first conformer: 4255 Chain: "b" Number of atoms: 5584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5584 Classifications: {'peptide': 693} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 31, 'TRANS': 661} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 11299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11299 Classifications: {'peptide': 1426} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 70, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 9046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 9046 Classifications: {'peptide': 1133} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1079} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 714 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain breaks: 1 Chain: "P" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 347 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "T" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 910 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2880 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 5 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10555 SG CYS A 111 113.909 81.327 51.331 1.00 52.15 S ATOM 10583 SG CYS A 114 117.229 82.747 49.279 1.00 60.58 S ATOM 10251 SG CYS A 71 117.165 91.345 97.668 1.00 41.25 S ATOM 10273 SG CYS A 74 114.935 94.491 97.391 1.00 35.32 S ATOM 10320 SG CYS A 81 113.304 91.119 98.041 1.00 35.83 S ATOM 29701 SG CYS B1119 110.915 100.763 84.229 1.00 32.24 S ATOM 29723 SG CYS B1122 111.619 99.058 81.411 1.00 35.98 S ATOM 29838 SG CYS B1137 113.735 99.087 84.418 1.00 48.78 S ATOM 30826 SG CYS C 88 76.737 83.301 153.147 1.00 27.25 S ATOM 30839 SG CYS C 90 80.056 81.822 152.095 1.00 37.75 S ATOM 30874 SG CYS C 94 77.965 80.187 154.753 1.00 23.11 S ATOM 30896 SG CYS C 97 76.790 79.964 151.165 1.00 16.65 S ATOM 38141 SG CYS I 17 86.878 20.552 46.341 1.00 39.89 S ATOM 38165 SG CYS I 20 89.969 21.958 48.150 1.00 41.99 S ATOM 38326 SG CYS I 39 88.046 24.330 46.114 1.00 38.99 S ATOM 38351 SG CYS I 42 89.820 21.280 44.417 1.00 43.23 S ATOM 38703 SG CYS I 86 50.488 18.419 71.599 1.00 32.07 S ATOM 38727 SG CYS I 89 50.726 15.597 73.521 1.00 31.64 S ATOM 38966 SG CYS I 119 54.061 16.332 73.572 1.00 38.63 S ATOM 40552 SG CYS L 22 103.535 44.333 134.183 1.00 35.66 S ATOM 40669 SG CYS L 36 106.377 46.423 134.669 1.00 37.97 S ATOM 42954 SG CYS Y 16 156.380 50.498 74.480 1.00 81.24 S ATOM 42976 SG CYS Y 19 154.286 48.516 71.755 1.00 84.47 S ATOM 43088 SG CYS Y 33 156.475 46.362 73.593 1.00 73.71 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N APRO a 7 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO a 7 " occ=0.50 residue: pdb=" N AGLY a 62 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY a 62 " occ=0.50 residue: pdb=" N AMET a 145 " occ=0.70 ... (14 atoms not shown) pdb=" CE BMET a 145 " occ=0.30 residue: pdb=" N GLU a 195 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU a 195 " occ=0.50 residue: pdb=" N ASP a 196 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP a 196 " occ=0.50 Time building chain proxies: 27.91, per 1000 atoms: 0.60 Number of scatterers: 46667 At special positions: 0 Unit cell: (214.774, 189.428, 186.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 285 16.00 P 98 15.00 Mg 1 11.99 O 8900 8.00 N 8143 7.00 C 29232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " Number of angles added : 15 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10496 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 66 sheets defined 36.0% alpha, 19.2% beta 26 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 16.69 Creating SS restraints... Processing helix chain 'a' and resid 32 through 36 Processing helix chain 'a' and resid 40 through 44 Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.705A pdb=" N LEU a 50 " --> pdb=" O HIS a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 81 Processing helix chain 'a' and resid 99 through 111 Processing helix chain 'a' and resid 130 through 146 Processing helix chain 'a' and resid 148 through 160 Processing helix chain 'a' and resid 166 through 178 Processing helix chain 'a' and resid 179 through 183 Processing helix chain 'a' and resid 190 through 195 removed outlier: 3.691A pdb=" N GLU a 195 " --> pdb=" O TRP a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 262 removed outlier: 3.877A pdb=" N GLY a 251 " --> pdb=" O GLN a 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU a 252 " --> pdb=" O PRO a 248 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 286 Processing helix chain 'a' and resid 371 through 375 Processing helix chain 'a' and resid 376 through 388 Processing helix chain 'a' and resid 388 through 395 removed outlier: 3.504A pdb=" N ARG a 392 " --> pdb=" O ILE a 388 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS a 395 " --> pdb=" O PRO a 391 " (cutoff:3.500A) Processing helix chain 'a' and resid 418 through 425 removed outlier: 4.055A pdb=" N LYS a 423 " --> pdb=" O CYS a 419 " (cutoff:3.500A) Processing helix chain 'a' and resid 461 through 464 Processing helix chain 'a' and resid 504 through 509 removed outlier: 4.146A pdb=" N GLN a 509 " --> pdb=" O LYS a 505 " (cutoff:3.500A) Processing helix chain 'a' and resid 538 through 551 Processing helix chain 'a' and resid 554 through 564 removed outlier: 4.120A pdb=" N ARG a 564 " --> pdb=" O GLU a 560 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 174 removed outlier: 4.188A pdb=" N ASP b 173 " --> pdb=" O GLU b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 205 Processing helix chain 'b' and resid 206 through 208 No H-bonds generated for 'chain 'b' and resid 206 through 208' Processing helix chain 'b' and resid 210 through 222 removed outlier: 3.530A pdb=" N ALA b 217 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG b 220 " --> pdb=" O ARG b 216 " (cutoff:3.500A) Processing helix chain 'b' and resid 224 through 228 removed outlier: 3.571A pdb=" N ILE b 227 " --> pdb=" O TYR b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 234 through 247 removed outlier: 4.328A pdb=" N MET b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE b 245 " --> pdb=" O ALA b 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 292 Processing helix chain 'b' and resid 309 through 313 Processing helix chain 'b' and resid 328 through 332 Processing helix chain 'b' and resid 338 through 352 Processing helix chain 'b' and resid 372 through 374 No H-bonds generated for 'chain 'b' and resid 372 through 374' Processing helix chain 'b' and resid 375 through 380 Processing helix chain 'b' and resid 380 through 394 Processing helix chain 'b' and resid 410 through 423 Processing helix chain 'b' and resid 453 through 470 Processing helix chain 'b' and resid 482 through 489 removed outlier: 3.579A pdb=" N ASP b 489 " --> pdb=" O VAL b 485 " (cutoff:3.500A) Processing helix chain 'b' and resid 489 through 520 Processing helix chain 'b' and resid 527 through 540 Processing helix chain 'b' and resid 553 through 563 Processing helix chain 'b' and resid 566 through 572 removed outlier: 3.771A pdb=" N TYR b 572 " --> pdb=" O ILE b 569 " (cutoff:3.500A) Processing helix chain 'b' and resid 581 through 586 Processing helix chain 'b' and resid 648 through 652 Processing helix chain 'b' and resid 675 through 690 Processing helix chain 'b' and resid 712 through 717 removed outlier: 3.797A pdb=" N PHE b 716 " --> pdb=" O MET b 712 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL b 717 " --> pdb=" O GLU b 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 712 through 717' Processing helix chain 'b' and resid 784 through 788 Processing helix chain 'b' and resid 790 through 797 Processing helix chain 'b' and resid 822 through 833 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.546A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.818A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.399A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.284A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.628A pdb=" N ASP A 437 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS A 439 " --> pdb=" O SER A 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.954A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.917A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.528A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.500A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.503A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.002A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.856A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 removed outlier: 3.524A pdb=" N ALA A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix removed outlier: 4.100A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 3.859A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1191 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.585A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 removed outlier: 3.988A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.886A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.718A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1435 through 1445 Processing helix chain 'A' and resid 1454 through 1461 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.720A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.169A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.751A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.829A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.276A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.577A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.704A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.657A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.559A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.996A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.581A pdb=" N MET B 764 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 873 through 877 removed outlier: 4.529A pdb=" N GLU B 877 " --> pdb=" O PRO B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.720A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.794A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.734A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.857A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.527A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 20' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.543A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR D 28 " --> pdb=" O GLU D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.596A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.879A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.523A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.305A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.561A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.737A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.868A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.148A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.678A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.822A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.898A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 5.748A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 203 removed outlier: 3.507A pdb=" N THR Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.597A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 3.561A pdb=" N LEU Z 245 " --> pdb=" O VAL Z 242 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.521A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing sheet with id=AA1, first strand: chain 'a' and resid 24 through 28 removed outlier: 3.927A pdb=" N CYS a 126 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU a 121 " --> pdb=" O MET a 61 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU a 63 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 241 through 243 removed outlier: 4.094A pdb=" N VAL a 310 " --> pdb=" O VAL a 322 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU a 341 " --> pdb=" O ILE a 364 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE a 364 " --> pdb=" O LEU a 341 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP a 343 " --> pdb=" O TYR a 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 271 through 275 removed outlier: 4.111A pdb=" N VAL a 274 " --> pdb=" O CYS a 453 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASP a 455 " --> pdb=" O VAL a 274 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ASP a 455 " --> pdb=" O PRO a 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY a 439 " --> pdb=" O LYS a 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 499 through 500 removed outlier: 3.766A pdb=" N ALA a 499 " --> pdb=" O LEU a 489 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL a 486 " --> pdb=" O THR a 474 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR a 474 " --> pdb=" O VAL a 486 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE a 514 " --> pdb=" O GLN a 529 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN a 529 " --> pdb=" O ILE a 514 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU a 516 " --> pdb=" O MET a 527 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 176 through 179 removed outlier: 6.724A pdb=" N VAL b 176 " --> pdb=" O ASN b 478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 321 through 323 removed outlier: 8.271A pdb=" N GLU b 322 " --> pdb=" O ALA b 295 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY b 297 " --> pdb=" O GLU b 322 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU b 271 " --> pdb=" O LYS b 296 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE b 298 " --> pdb=" O LEU b 271 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE b 273 " --> pdb=" O PHE b 298 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N MET b 300 " --> pdb=" O PHE b 273 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP b 275 " --> pdb=" O MET b 300 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N TYR b 272 " --> pdb=" O HIS b 359 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU b 361 " --> pdb=" O TYR b 272 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA b 274 " --> pdb=" O LEU b 361 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA b 363 " --> pdb=" O ALA b 274 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL b 276 " --> pdb=" O ALA b 363 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL b 358 " --> pdb=" O ARG b 396 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLY b 398 " --> pdb=" O VAL b 358 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N PHE b 360 " --> pdb=" O GLY b 398 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS b 400 " --> pdb=" O PHE b 360 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET b 362 " --> pdb=" O HIS b 400 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE b 402 " --> pdb=" O MET b 362 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY b 399 " --> pdb=" O GLY b 448 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU b 449 " --> pdb=" O PHE b 424 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE b 424 " --> pdb=" O LEU b 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 575 through 576 removed outlier: 6.117A pdb=" N THR b 575 " --> pdb=" O PHE b 800 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU b 802 " --> pdb=" O THR b 575 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY b 747 " --> pdb=" O SER b 596 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 623 through 624 removed outlier: 6.388A pdb=" N SER b 638 " --> pdb=" O VAL b 663 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL b 663 " --> pdb=" O SER b 638 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLU b 640 " --> pdb=" O LEU b 661 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU b 661 " --> pdb=" O GLU b 640 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL b 642 " --> pdb=" O HIS b 659 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS b 659 " --> pdb=" O VAL b 642 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU b 644 " --> pdb=" O ALA b 657 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA b 657 " --> pdb=" O GLU b 644 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS b 646 " --> pdb=" O ILE b 655 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE b 655 " --> pdb=" O LYS b 646 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 623 through 624 removed outlier: 6.388A pdb=" N SER b 638 " --> pdb=" O VAL b 663 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL b 663 " --> pdb=" O SER b 638 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLU b 640 " --> pdb=" O LEU b 661 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU b 661 " --> pdb=" O GLU b 640 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL b 642 " --> pdb=" O HIS b 659 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS b 659 " --> pdb=" O VAL b 642 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU b 644 " --> pdb=" O ALA b 657 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA b 657 " --> pdb=" O GLU b 644 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS b 646 " --> pdb=" O ILE b 655 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE b 655 " --> pdb=" O LYS b 646 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 719 through 723 Processing sheet with id=AB2, first strand: chain 'b' and resid 758 through 763 Processing sheet with id=AB3, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.537A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AB6, first strand: chain 'A' and resid 192 through 194 Processing sheet with id=AB7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.699A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.547A pdb=" N SER A 362 " --> pdb=" O ARG B1062 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.706A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.693A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AC3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.605A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 965 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.224A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC8, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AC9, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.650A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 3.907A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AD3, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AD4, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AD5, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.058A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.509A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD8, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.349A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.334A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AE2, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AE3, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.189A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.753A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.753A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET L 15 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AE7, first strand: chain 'B' and resid 827 through 829 removed outlier: 7.359A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.616A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AF1, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AF2, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.920A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.390A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AF5, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.731A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.731A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 102 through 105 Processing sheet with id=AF8, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.131A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.639A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 159 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AG2, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.785A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AG4, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AG5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AG6, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AG7, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.143A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 372 through 377 removed outlier: 8.404A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG Z 280 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE Z 382 " --> pdb=" O ARG Z 280 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 352 through 355 Processing sheet with id=AH1, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AH2, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.364A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.971A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1838 hydrogen bonds defined for protein. 5035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 25.34 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14526 1.34 - 1.46: 7105 1.46 - 1.57: 25521 1.57 - 1.69: 193 1.69 - 1.81: 448 Bond restraints: 47793 Sorted by residual: bond pdb=" CE3 TRP b 293 " pdb=" CZ3 TRP b 293 " ideal model delta sigma weight residual 1.382 1.312 0.070 3.00e-02 1.11e+03 5.51e+00 bond pdb=" CG LEU b 666 " pdb=" CD2 LEU b 666 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.69e+00 bond pdb=" CB GLU b 322 " pdb=" CG GLU b 322 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" CB PRO b 757 " pdb=" CG PRO b 757 " ideal model delta sigma weight residual 1.492 1.584 -0.092 5.00e-02 4.00e+02 3.38e+00 bond pdb=" CB PRO a 162 " pdb=" CG PRO a 162 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.30e+00 ... (remaining 47788 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 63846 1.72 - 3.45: 976 3.45 - 5.17: 119 5.17 - 6.90: 32 6.90 - 8.62: 3 Bond angle restraints: 64976 Sorted by residual: angle pdb=" C GLY A1120 " pdb=" N VAL A1121 " pdb=" CA VAL A1121 " ideal model delta sigma weight residual 120.24 123.40 -3.16 6.30e-01 2.52e+00 2.52e+01 angle pdb=" N GLY b 668 " pdb=" CA GLY b 668 " pdb=" C GLY b 668 " ideal model delta sigma weight residual 113.58 118.74 -5.16 1.07e+00 8.73e-01 2.32e+01 angle pdb=" CA TYR a 362 " pdb=" CB TYR a 362 " pdb=" CG TYR a 362 " ideal model delta sigma weight residual 113.90 122.52 -8.62 1.80e+00 3.09e-01 2.29e+01 angle pdb=" N ILE B 423 " pdb=" CA ILE B 423 " pdb=" C ILE B 423 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" N GLN B 631 " pdb=" CA GLN B 631 " pdb=" C GLN B 631 " ideal model delta sigma weight residual 112.97 108.66 4.31 1.06e+00 8.90e-01 1.66e+01 ... (remaining 64971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 28017 35.64 - 71.28: 871 71.28 - 106.92: 34 106.92 - 142.56: 5 142.56 - 178.20: 2 Dihedral angle restraints: 28929 sinusoidal: 12691 harmonic: 16238 Sorted by residual: dihedral pdb=" C8 GTP P 101 " pdb=" C1' GTP P 101 " pdb=" N9 GTP P 101 " pdb=" O4' GTP P 101 " ideal model delta sinusoidal sigma weight residual 104.59 -33.26 137.85 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" O3A GTP P 101 " pdb=" O3B GTP P 101 " pdb=" PB GTP P 101 " pdb=" PG GTP P 101 " ideal model delta sinusoidal sigma weight residual -56.21 -169.59 113.39 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" O3B GTP P 101 " pdb=" O3A GTP P 101 " pdb=" PB GTP P 101 " pdb=" PA GTP P 101 " ideal model delta sinusoidal sigma weight residual 291.08 178.22 112.86 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 28926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 5400 0.042 - 0.085: 1307 0.085 - 0.127: 467 0.127 - 0.170: 29 0.170 - 0.212: 3 Chirality restraints: 7206 Sorted by residual: chirality pdb=" CA PRO b 757 " pdb=" N PRO b 757 " pdb=" C PRO b 757 " pdb=" CB PRO b 757 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO b 280 " pdb=" N PRO b 280 " pdb=" C PRO b 280 " pdb=" CB PRO b 280 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN C 190 " pdb=" N ASN C 190 " pdb=" C ASN C 190 " pdb=" CB ASN C 190 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 7203 not shown) Planarity restraints: 8075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO a 161 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.21e+01 pdb=" N PRO a 162 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO a 162 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO a 162 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY b 279 " 0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO b 280 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO b 280 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO b 280 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU b 756 " 0.063 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO b 757 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO b 757 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO b 757 " 0.052 5.00e-02 4.00e+02 ... (remaining 8072 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 220 2.52 - 3.11: 33789 3.11 - 3.71: 73627 3.71 - 4.30: 106077 4.30 - 4.90: 173449 Nonbonded interactions: 387162 Sorted by model distance: nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 1.923 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 1.934 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.010 2.170 nonbonded pdb=" NZ LYS b 725 " pdb=" O VAL G 136 " model vdw 2.107 3.120 nonbonded pdb=" OG SER B 480 " pdb=" OD1 ASN B 525 " model vdw 2.180 3.040 ... (remaining 387157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 1.990 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: 1.740 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 129.010 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.180 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 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 : 0.002 0.092 47793 Z= 0.153 Angle : 0.540 8.623 64976 Z= 0.293 Chirality : 0.042 0.212 7206 Planarity : 0.004 0.117 8075 Dihedral : 14.710 178.202 18433 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 3.62 % Allowed : 5.71 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.11), residues: 5529 helix: 0.25 (0.12), residues: 1772 sheet: -1.27 (0.17), residues: 855 loop : -1.16 (0.11), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP b 293 HIS 0.005 0.001 HIS a 435 PHE 0.020 0.001 PHE a 329 TYR 0.016 0.001 TYR b 421 ARG 0.005 0.000 ARG a 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1021 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 385 GLU cc_start: 0.3097 (OUTLIER) cc_final: 0.2784 (tp30) REVERT: a 418 ILE cc_start: -0.4637 (OUTLIER) cc_final: -0.5624 (mm) REVERT: b 182 MET cc_start: 0.2980 (mmt) cc_final: 0.2238 (mmp) REVERT: b 250 MET cc_start: 0.1501 (ttt) cc_final: 0.0415 (mtp) REVERT: b 496 MET cc_start: -0.2748 (tpt) cc_final: -0.3675 (tpt) REVERT: b 712 MET cc_start: 0.5145 (ttm) cc_final: 0.4616 (ttp) REVERT: b 813 GLN cc_start: -0.3887 (OUTLIER) cc_final: -0.4267 (pt0) REVERT: b 816 GLN cc_start: 0.0419 (OUTLIER) cc_final: 0.0122 (tp40) REVERT: A 205 VAL cc_start: 0.6298 (OUTLIER) cc_final: 0.5352 (m) REVERT: A 224 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7065 (pt) REVERT: A 464 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7348 (mp) REVERT: A 467 MET cc_start: 0.5818 (mpt) cc_final: 0.4747 (mmm) REVERT: A 515 ILE cc_start: 0.8406 (mm) cc_final: 0.8158 (mt) REVERT: A 585 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 857 THR cc_start: 0.7826 (p) cc_final: 0.7592 (t) REVERT: A 1016 LEU cc_start: 0.7702 (tp) cc_final: 0.7374 (tp) REVERT: A 1043 ILE cc_start: 0.8247 (mt) cc_final: 0.7431 (mt) REVERT: A 1191 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.4066 (tm-30) REVERT: B 403 LEU cc_start: 0.7417 (tp) cc_final: 0.6720 (tt) REVERT: B 448 LEU cc_start: 0.7565 (mt) cc_final: 0.7271 (mt) REVERT: B 604 ILE cc_start: 0.8213 (mp) cc_final: 0.7900 (mp) REVERT: B 614 ILE cc_start: 0.7133 (mt) cc_final: 0.6616 (mt) REVERT: B 784 SER cc_start: 0.8197 (m) cc_final: 0.7896 (p) REVERT: B 801 VAL cc_start: 0.7892 (t) cc_final: 0.7678 (t) REVERT: B 1103 LEU cc_start: 0.8480 (tp) cc_final: 0.8136 (tp) REVERT: E 194 ILE cc_start: 0.8679 (mp) cc_final: 0.8327 (mt) REVERT: F 60 TYR cc_start: 0.7558 (m-80) cc_final: 0.6384 (m-80) REVERT: F 112 ASP cc_start: 0.6366 (p0) cc_final: 0.6126 (p0) REVERT: H 58 LEU cc_start: 0.5425 (tt) cc_final: 0.5155 (tt) REVERT: H 59 VAL cc_start: 0.8592 (t) cc_final: 0.8336 (t) outliers start: 177 outliers final: 26 residues processed: 1168 average time/residue: 0.6096 time to fit residues: 1159.9798 Evaluate side-chains 582 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 547 time to evaluate : 5.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 322 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 385 GLU Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 418 ILE Chi-restraints excluded: chain a residue 475 ARG Chi-restraints excluded: chain a residue 486 VAL Chi-restraints excluded: chain a residue 510 TYR Chi-restraints excluded: chain a residue 528 ARG Chi-restraints excluded: chain b residue 290 ARG Chi-restraints excluded: chain b residue 310 LEU Chi-restraints excluded: chain b residue 383 LEU Chi-restraints excluded: chain b residue 509 LYS Chi-restraints excluded: chain b residue 532 ARG Chi-restraints excluded: chain b residue 813 GLN Chi-restraints excluded: chain b residue 816 GLN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1202 PHE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain K residue 80 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 471 optimal weight: 10.0000 chunk 422 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 437 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 506 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 102 ASN a 158 GLN a 243 GLN a 272 GLN ** a 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 484 GLN b 677 ASN b 678 GLN ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 293 ASN A 311 GLN A 330 GLN A 377 GLN A 387 ASN A 507 GLN A 609 HIS A 654 HIS A 780 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 825 ASN A 905 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN A1129 ASN A1244 ASN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1410 HIS ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 GLN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 552 ASN B 577 HIS B 585 ASN B 593 GLN B 631 GLN B 639 HIS B 649 ASN B 650 ASN ** B 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 GLN B 755 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN B 980 HIS B 986 GLN B1003 ASN B1053 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN B1145 GLN C 55 ASN C 232 ASN D 135 GLN ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 76 ASN H 87 GLN H 126 GLN I 22 ASN I 45 GLN I 84 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 HIS Z 178 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 47793 Z= 0.458 Angle : 0.804 10.796 64976 Z= 0.421 Chirality : 0.047 0.234 7206 Planarity : 0.006 0.115 8075 Dihedral : 15.540 177.378 7262 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.15 % Allowed : 12.75 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.11), residues: 5529 helix: 0.36 (0.12), residues: 1805 sheet: -1.09 (0.17), residues: 815 loop : -0.95 (0.12), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1192 HIS 0.011 0.002 HIS B 387 PHE 0.030 0.002 PHE A1239 TYR 0.027 0.002 TYR L 41 ARG 0.018 0.001 ARG b 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 495 time to evaluate : 5.110 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: a 61 MET cc_start: -0.0886 (mtp) cc_final: -0.1447 (mtt) REVERT: a 276 MET cc_start: -0.0367 (mtp) cc_final: -0.0985 (mtm) REVERT: a 437 MET cc_start: -0.0334 (ptp) cc_final: -0.2442 (ttt) REVERT: a 486 VAL cc_start: 0.3597 (OUTLIER) cc_final: 0.3234 (p) REVERT: b 182 MET cc_start: 0.3412 (mmt) cc_final: 0.2443 (mmp) REVERT: b 250 MET cc_start: 0.1431 (ttt) cc_final: 0.0124 (mtp) REVERT: b 496 MET cc_start: -0.3100 (tpt) cc_final: -0.3739 (tpt) REVERT: b 712 MET cc_start: 0.4673 (ttm) cc_final: 0.3775 (ttp) REVERT: b 813 GLN cc_start: -0.4543 (OUTLIER) cc_final: -0.5063 (pt0) REVERT: A 346 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8087 (tttt) REVERT: A 585 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 637 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7469 (ptp) REVERT: A 717 ILE cc_start: 0.8433 (mt) cc_final: 0.8231 (mt) REVERT: A 1191 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: A 1451 MET cc_start: 0.7147 (mtp) cc_final: 0.6904 (mtp) REVERT: B 108 MET cc_start: 0.4855 (tpp) cc_final: 0.4336 (tpp) REVERT: B 163 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8212 (pp) REVERT: B 529 MET cc_start: 0.7431 (mmm) cc_final: 0.6875 (mmm) REVERT: B 603 MET cc_start: 0.7264 (mpp) cc_final: 0.6753 (mmp) REVERT: B 604 ILE cc_start: 0.8694 (mp) cc_final: 0.8477 (mp) REVERT: B 709 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8222 (t) REVERT: B 764 MET cc_start: 0.7370 (mmm) cc_final: 0.7135 (mmm) REVERT: B 1054 MET cc_start: 0.8169 (mpp) cc_final: 0.7588 (mtm) REVERT: E 194 ILE cc_start: 0.8916 (mp) cc_final: 0.8599 (mt) REVERT: F 112 ASP cc_start: 0.6659 (p0) cc_final: 0.6209 (p0) REVERT: F 121 ASP cc_start: 0.6656 (p0) cc_final: 0.6386 (p0) REVERT: H 118 TYR cc_start: 0.7416 (m-80) cc_final: 0.7162 (m-80) REVERT: Y 48 MET cc_start: 0.1160 (tpt) cc_final: -0.0544 (ttp) REVERT: Z 447 LYS cc_start: 0.4766 (OUTLIER) cc_final: 0.4501 (tptp) outliers start: 203 outliers final: 109 residues processed: 658 average time/residue: 0.5861 time to fit residues: 641.4594 Evaluate side-chains 525 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 407 time to evaluate : 5.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 HIS Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 322 VAL Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 475 ARG Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain a residue 486 VAL Chi-restraints excluded: chain a residue 504 THR Chi-restraints excluded: chain a residue 510 TYR Chi-restraints excluded: chain a residue 528 ARG Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 383 LEU Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain b residue 813 GLN Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 203 LYS Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1472 ASP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 281 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 421 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 507 optimal weight: 10.0000 chunk 548 optimal weight: 0.7980 chunk 452 optimal weight: 10.0000 chunk 503 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 407 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 102 ASN ** b 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 294 HIS ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1082 HIS A1101 GLN ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1457 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 481 HIS B 593 GLN B 699 HIS ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 111 GLN E 132 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 47793 Z= 0.304 Angle : 0.690 12.740 64976 Z= 0.355 Chirality : 0.045 0.281 7206 Planarity : 0.005 0.114 8075 Dihedral : 15.306 176.657 7229 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.14 % Rotamer: Outliers : 3.15 % Allowed : 14.15 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.11), residues: 5529 helix: 0.58 (0.12), residues: 1793 sheet: -1.11 (0.17), residues: 845 loop : -0.86 (0.12), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1192 HIS 0.011 0.001 HIS A 465 PHE 0.024 0.002 PHE B 356 TYR 0.029 0.002 TYR B 887 ARG 0.013 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 437 time to evaluate : 5.437 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: a 61 MET cc_start: -0.0972 (mtp) cc_final: -0.1302 (mtt) REVERT: a 276 MET cc_start: -0.0307 (mtp) cc_final: -0.0656 (mtt) REVERT: a 437 MET cc_start: -0.0788 (ptp) cc_final: -0.2772 (ttt) REVERT: b 250 MET cc_start: 0.1393 (ttt) cc_final: 0.0080 (mtp) REVERT: b 496 MET cc_start: -0.3087 (tpt) cc_final: -0.3561 (tpt) REVERT: b 721 MET cc_start: 0.6897 (tpp) cc_final: 0.6208 (tpp) REVERT: b 813 GLN cc_start: -0.4959 (OUTLIER) cc_final: -0.5315 (pt0) REVERT: A 191 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6054 (mt) REVERT: A 524 MET cc_start: 0.6692 (tpp) cc_final: 0.6359 (mmt) REVERT: A 637 MET cc_start: 0.7721 (ptp) cc_final: 0.7461 (ptp) REVERT: A 1191 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7037 (pm20) REVERT: A 1460 LEU cc_start: 0.8233 (mp) cc_final: 0.7923 (mt) REVERT: B 603 MET cc_start: 0.7121 (mpp) cc_final: 0.6576 (mpp) REVERT: B 1054 MET cc_start: 0.8181 (mpp) cc_final: 0.7575 (mpp) REVERT: E 194 ILE cc_start: 0.8917 (mp) cc_final: 0.8663 (mt) REVERT: E 208 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8359 (tt) REVERT: F 66 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8051 (mm) REVERT: F 112 ASP cc_start: 0.6793 (p0) cc_final: 0.6400 (p0) REVERT: F 121 ASP cc_start: 0.5809 (p0) cc_final: 0.5511 (p0) REVERT: G 31 PHE cc_start: 0.5767 (m-80) cc_final: 0.5557 (m-80) REVERT: H 118 TYR cc_start: 0.7317 (m-80) cc_final: 0.6938 (m-80) REVERT: K 61 TYR cc_start: 0.9189 (p90) cc_final: 0.8886 (p90) REVERT: Z 447 LYS cc_start: 0.4306 (OUTLIER) cc_final: 0.3426 (tptp) outliers start: 153 outliers final: 94 residues processed: 557 average time/residue: 0.5776 time to fit residues: 542.0363 Evaluate side-chains 489 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 389 time to evaluate : 5.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 HIS Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain a residue 486 VAL Chi-restraints excluded: chain a residue 510 TYR Chi-restraints excluded: chain b residue 383 LEU Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain b residue 813 GLN Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1167 ARG Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 366 TYR Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 501 optimal weight: 1.9990 chunk 381 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 242 optimal weight: 4.9990 chunk 340 optimal weight: 8.9990 chunk 509 optimal weight: 5.9990 chunk 539 optimal weight: 50.0000 chunk 266 optimal weight: 5.9990 chunk 482 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 242 ASN ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN B1094 GLN E 169 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS J 52 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 47793 Z= 0.261 Angle : 0.666 12.609 64976 Z= 0.339 Chirality : 0.044 0.234 7206 Planarity : 0.005 0.112 8075 Dihedral : 15.047 177.291 7214 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.95 % Favored : 94.96 % Rotamer: Outliers : 3.42 % Allowed : 14.64 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5529 helix: 0.77 (0.12), residues: 1783 sheet: -1.01 (0.17), residues: 837 loop : -0.79 (0.12), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.010 0.001 HIS A 465 PHE 0.018 0.001 PHE a 526 TYR 0.020 0.002 TYR F 60 ARG 0.018 0.000 ARG a 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 413 time to evaluate : 5.188 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: a 437 MET cc_start: -0.0635 (ptp) cc_final: -0.2764 (ttt) REVERT: b 175 MET cc_start: 0.4819 (mmm) cc_final: 0.2884 (mmt) REVERT: b 250 MET cc_start: 0.1321 (ttt) cc_final: 0.0012 (mtp) REVERT: b 496 MET cc_start: -0.3139 (tpt) cc_final: -0.3613 (tpt) REVERT: b 712 MET cc_start: 0.4743 (ttm) cc_final: 0.4173 (ttp) REVERT: b 721 MET cc_start: 0.6980 (tpp) cc_final: 0.6331 (tpp) REVERT: A 85 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6572 (t80) REVERT: A 318 VAL cc_start: 0.7154 (t) cc_final: 0.6944 (t) REVERT: A 467 MET cc_start: 0.6110 (mmt) cc_final: 0.5703 (mmp) REVERT: A 687 ILE cc_start: 0.8831 (tp) cc_final: 0.8423 (mt) REVERT: A 1191 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6973 (pm20) REVERT: A 1192 TRP cc_start: 0.6422 (OUTLIER) cc_final: 0.6119 (p-90) REVERT: A 1460 LEU cc_start: 0.8456 (mp) cc_final: 0.8184 (mt) REVERT: B 508 MET cc_start: 0.8128 (mmp) cc_final: 0.7922 (mmp) REVERT: B 779 ILE cc_start: 0.9131 (mm) cc_final: 0.8397 (tt) REVERT: B 840 MET cc_start: 0.5225 (tpp) cc_final: 0.4956 (mmm) REVERT: B 1054 MET cc_start: 0.8223 (mpp) cc_final: 0.7756 (mtm) REVERT: B 1163 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6876 (mtp) REVERT: E 208 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8347 (tt) REVERT: F 112 ASP cc_start: 0.6150 (p0) cc_final: 0.5830 (p0) REVERT: H 118 TYR cc_start: 0.7234 (m-80) cc_final: 0.6986 (m-80) REVERT: Y 48 MET cc_start: 0.1157 (tpt) cc_final: -0.0025 (ttp) REVERT: Z 447 LYS cc_start: 0.4033 (OUTLIER) cc_final: 0.2993 (tptp) outliers start: 166 outliers final: 105 residues processed: 545 average time/residue: 0.5732 time to fit residues: 527.7080 Evaluate side-chains 491 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 380 time to evaluate : 5.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 HIS Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain a residue 486 VAL Chi-restraints excluded: chain a residue 510 TYR Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1192 TRP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 366 TYR Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 449 optimal weight: 7.9990 chunk 306 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 401 optimal weight: 0.9980 chunk 222 optimal weight: 0.5980 chunk 460 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 chunk 0 optimal weight: 80.0000 chunk 275 optimal weight: 3.9990 chunk 484 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 280 ASN a 393 HIS ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 47793 Z= 0.266 Angle : 0.658 10.667 64976 Z= 0.337 Chirality : 0.044 0.226 7206 Planarity : 0.005 0.111 8075 Dihedral : 14.850 178.622 7205 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.52 % Allowed : 15.27 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 5529 helix: 0.94 (0.12), residues: 1785 sheet: -0.95 (0.17), residues: 854 loop : -0.69 (0.12), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 27 HIS 0.007 0.001 HIS b 833 PHE 0.014 0.001 PHE A 225 TYR 0.024 0.002 TYR K 61 ARG 0.007 0.000 ARG A1167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 396 time to evaluate : 4.758 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: a 276 MET cc_start: -0.1221 (mtt) cc_final: -0.1600 (mpp) REVERT: a 437 MET cc_start: -0.0616 (ptp) cc_final: -0.2758 (ttt) REVERT: b 250 MET cc_start: 0.1257 (ttt) cc_final: -0.0073 (mtp) REVERT: b 300 MET cc_start: 0.0984 (tpt) cc_final: 0.0358 (tpt) REVERT: b 496 MET cc_start: -0.3127 (tpt) cc_final: -0.3393 (tpt) REVERT: b 712 MET cc_start: 0.4290 (ttm) cc_final: 0.3653 (ttp) REVERT: b 721 MET cc_start: 0.7205 (tpp) cc_final: 0.6489 (tpp) REVERT: A 687 ILE cc_start: 0.8832 (tp) cc_final: 0.8439 (mt) REVERT: A 1133 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7579 (pttp) REVERT: A 1191 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: B 779 ILE cc_start: 0.9148 (mm) cc_final: 0.8439 (tt) REVERT: B 1054 MET cc_start: 0.8205 (mpp) cc_final: 0.7654 (mtm) REVERT: E 208 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8374 (tt) REVERT: F 66 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8033 (mm) REVERT: F 112 ASP cc_start: 0.6131 (p0) cc_final: 0.5808 (p0) REVERT: H 118 TYR cc_start: 0.7188 (m-80) cc_final: 0.6312 (m-80) REVERT: Y 48 MET cc_start: 0.1066 (tpt) cc_final: 0.0026 (ttp) REVERT: Z 447 LYS cc_start: 0.3611 (OUTLIER) cc_final: 0.2707 (mmmt) outliers start: 171 outliers final: 117 residues processed: 535 average time/residue: 0.5536 time to fit residues: 499.6864 Evaluate side-chains 477 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 355 time to evaluate : 4.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 HIS Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain a residue 486 VAL Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1219 LYS Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1094 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 366 TYR Chi-restraints excluded: chain Z residue 447 LYS Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 181 optimal weight: 3.9990 chunk 485 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 316 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 539 optimal weight: 50.0000 chunk 448 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 283 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 723 ASN ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1313 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 168 ASN E 169 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN K 76 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 47793 Z= 0.188 Angle : 0.654 13.718 64976 Z= 0.328 Chirality : 0.044 0.242 7206 Planarity : 0.004 0.109 8075 Dihedral : 14.731 178.720 7203 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.93 % Allowed : 16.24 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 5529 helix: 1.09 (0.13), residues: 1780 sheet: -0.89 (0.17), residues: 837 loop : -0.58 (0.12), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.001 TRP A1192 HIS 0.006 0.001 HIS B 350 PHE 0.015 0.001 PHE A 85 TYR 0.020 0.001 TYR E 125 ARG 0.007 0.000 ARG A1167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 397 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 61 MET cc_start: -0.2232 (mtt) cc_final: -0.2463 (mpp) REVERT: a 276 MET cc_start: -0.1127 (mtt) cc_final: -0.1510 (mpp) REVERT: a 437 MET cc_start: -0.0684 (ptp) cc_final: -0.2614 (ttt) REVERT: b 171 MET cc_start: -0.4198 (mmt) cc_final: -0.4844 (mmp) REVERT: b 175 MET cc_start: 0.4464 (mmm) cc_final: 0.3083 (mmt) REVERT: b 226 MET cc_start: 0.2367 (pmm) cc_final: 0.2055 (pmm) REVERT: b 250 MET cc_start: 0.1586 (ttt) cc_final: 0.0132 (mtp) REVERT: b 300 MET cc_start: 0.0914 (tpt) cc_final: 0.0276 (tpt) REVERT: b 496 MET cc_start: -0.3248 (tpt) cc_final: -0.3499 (tpt) REVERT: b 712 MET cc_start: 0.4159 (ttm) cc_final: 0.3483 (ttp) REVERT: b 721 MET cc_start: 0.7181 (tpp) cc_final: 0.6462 (tpp) REVERT: A 1191 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: A 1321 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 779 ILE cc_start: 0.9117 (mm) cc_final: 0.8459 (tt) REVERT: B 1054 MET cc_start: 0.8115 (mpp) cc_final: 0.7824 (mtm) REVERT: E 208 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8373 (tt) REVERT: F 112 ASP cc_start: 0.6357 (p0) cc_final: 0.6036 (p0) REVERT: H 118 TYR cc_start: 0.7574 (m-80) cc_final: 0.7163 (m-80) REVERT: Y 48 MET cc_start: 0.1007 (tpt) cc_final: 0.0768 (ttt) REVERT: Z 254 MET cc_start: 0.0326 (mmm) cc_final: 0.0089 (mmm) outliers start: 142 outliers final: 90 residues processed: 508 average time/residue: 0.4835 time to fit residues: 413.8916 Evaluate side-chains 462 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 369 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 992 ASN Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1088 GLU Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1094 GLN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 520 optimal weight: 0.0970 chunk 60 optimal weight: 40.0000 chunk 307 optimal weight: 0.6980 chunk 394 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 454 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 537 optimal weight: 50.0000 chunk 336 optimal weight: 4.9990 chunk 327 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN E 168 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 47793 Z= 0.213 Angle : 0.661 13.315 64976 Z= 0.331 Chirality : 0.044 0.417 7206 Planarity : 0.004 0.107 8075 Dihedral : 14.605 179.935 7202 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 2.46 % Allowed : 16.95 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 5529 helix: 1.13 (0.13), residues: 1781 sheet: -0.85 (0.17), residues: 850 loop : -0.54 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1192 HIS 0.012 0.001 HIS a 46 PHE 0.014 0.001 PHE A 85 TYR 0.019 0.001 TYR B 949 ARG 0.011 0.000 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 383 time to evaluate : 4.974 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: a 61 MET cc_start: -0.2257 (mtt) cc_final: -0.2593 (mpp) REVERT: a 276 MET cc_start: -0.1059 (mtt) cc_final: -0.1716 (mpp) REVERT: a 437 MET cc_start: -0.0589 (ptp) cc_final: -0.2555 (ttt) REVERT: b 171 MET cc_start: -0.4519 (mmt) cc_final: -0.5058 (mmp) REVERT: b 175 MET cc_start: 0.4616 (mmm) cc_final: 0.4069 (mmt) REVERT: b 226 MET cc_start: 0.2473 (pmm) cc_final: 0.2247 (pmm) REVERT: b 250 MET cc_start: 0.1568 (ttt) cc_final: 0.0098 (mtp) REVERT: b 300 MET cc_start: 0.0819 (tpt) cc_final: 0.0251 (tpt) REVERT: b 496 MET cc_start: -0.3334 (tpt) cc_final: -0.3863 (tpt) REVERT: b 712 MET cc_start: 0.4159 (ttm) cc_final: 0.3454 (ttp) REVERT: b 721 MET cc_start: 0.7185 (tpp) cc_final: 0.6923 (tpp) REVERT: A 400 ASP cc_start: 0.6820 (p0) cc_final: 0.6614 (p0) REVERT: A 469 MET cc_start: 0.7539 (tpp) cc_final: 0.7016 (tpp) REVERT: A 841 MET cc_start: 0.7832 (mtt) cc_final: 0.7603 (ttm) REVERT: A 863 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7668 (mtp85) REVERT: A 1191 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: A 1321 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (mp) REVERT: B 719 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7734 (m) REVERT: B 779 ILE cc_start: 0.9108 (mm) cc_final: 0.8485 (tt) REVERT: B 1054 MET cc_start: 0.8099 (mpp) cc_final: 0.7775 (mtm) REVERT: E 208 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8308 (tt) REVERT: F 112 ASP cc_start: 0.6418 (p0) cc_final: 0.6068 (p0) REVERT: H 118 TYR cc_start: 0.7590 (m-80) cc_final: 0.7228 (m-80) outliers start: 119 outliers final: 93 residues processed: 479 average time/residue: 0.6048 time to fit residues: 487.3586 Evaluate side-chains 460 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 362 time to evaluate : 5.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain b residue 182 MET Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1197 TYR Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 752 TYR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain B residue 1094 GLN Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 332 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 341 optimal weight: 8.9990 chunk 366 optimal weight: 6.9990 chunk 265 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 422 optimal weight: 0.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 460 HIS B 525 ASN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 47793 Z= 0.333 Angle : 0.715 12.801 64976 Z= 0.362 Chirality : 0.045 0.325 7206 Planarity : 0.005 0.106 8075 Dihedral : 14.559 178.056 7202 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 3.09 % Allowed : 16.81 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5529 helix: 0.99 (0.12), residues: 1799 sheet: -0.88 (0.17), residues: 858 loop : -0.58 (0.12), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1192 HIS 0.007 0.001 HIS B1053 PHE 0.019 0.002 PHE A 85 TYR 0.035 0.002 TYR K 61 ARG 0.007 0.001 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 356 time to evaluate : 5.552 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: a 276 MET cc_start: -0.1078 (mtt) cc_final: -0.1703 (mpp) REVERT: a 437 MET cc_start: -0.0464 (ptp) cc_final: -0.2497 (ttt) REVERT: b 171 MET cc_start: -0.4471 (mmt) cc_final: -0.4967 (mmp) REVERT: b 175 MET cc_start: 0.4524 (mmm) cc_final: 0.3990 (mmt) REVERT: b 250 MET cc_start: 0.1536 (ttt) cc_final: 0.1226 (ttm) REVERT: b 300 MET cc_start: 0.0963 (tpt) cc_final: 0.0339 (tpt) REVERT: b 496 MET cc_start: -0.3301 (tpt) cc_final: -0.3860 (tpt) REVERT: b 712 MET cc_start: 0.4290 (ttm) cc_final: 0.3324 (ttp) REVERT: b 721 MET cc_start: 0.7283 (tpp) cc_final: 0.7015 (tpp) REVERT: A 339 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6668 (mt) REVERT: A 469 MET cc_start: 0.7796 (tpp) cc_final: 0.7330 (tpp) REVERT: A 863 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: A 1191 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: B 550 MET cc_start: 0.8571 (tmm) cc_final: 0.7704 (tmm) REVERT: B 779 ILE cc_start: 0.9129 (mm) cc_final: 0.8662 (tp) REVERT: B 840 MET cc_start: 0.4455 (tpp) cc_final: 0.3877 (tpp) REVERT: E 208 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8410 (tt) REVERT: F 66 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (mm) REVERT: F 112 ASP cc_start: 0.6321 (p0) cc_final: 0.5923 (p0) REVERT: L 44 MET cc_start: 0.6834 (mmm) cc_final: 0.6488 (mmm) outliers start: 150 outliers final: 108 residues processed: 477 average time/residue: 0.5853 time to fit residues: 472.2000 Evaluate side-chains 458 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 345 time to evaluate : 5.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain a residue 482 LEU Chi-restraints excluded: chain b residue 182 MET Chi-restraints excluded: chain b residue 362 MET Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain b residue 634 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 863 ARG Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1199 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 621 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 961 ILE Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1089 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 11 PHE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 489 optimal weight: 0.9990 chunk 515 optimal weight: 30.0000 chunk 470 optimal weight: 5.9990 chunk 501 optimal weight: 0.8980 chunk 301 optimal weight: 0.0980 chunk 218 optimal weight: 0.8980 chunk 393 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 452 optimal weight: 0.6980 chunk 474 optimal weight: 7.9990 chunk 499 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 699 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 287 HIS ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS Y 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 47793 Z= 0.190 Angle : 0.696 14.350 64976 Z= 0.342 Chirality : 0.045 0.264 7206 Planarity : 0.004 0.105 8075 Dihedral : 14.474 179.536 7202 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.82 % Favored : 95.09 % Rotamer: Outliers : 1.91 % Allowed : 18.24 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 5529 helix: 1.11 (0.13), residues: 1786 sheet: -0.82 (0.17), residues: 877 loop : -0.50 (0.12), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1192 HIS 0.009 0.001 HIS B 350 PHE 0.018 0.001 PHE G 44 TYR 0.021 0.001 TYR J 21 ARG 0.007 0.000 ARG A1167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 382 time to evaluate : 5.485 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: a 276 MET cc_start: -0.1548 (mtt) cc_final: -0.2059 (mpp) REVERT: a 437 MET cc_start: -0.0001 (ptp) cc_final: -0.2270 (ttt) REVERT: b 171 MET cc_start: -0.4484 (mmt) cc_final: -0.4970 (mmp) REVERT: b 175 MET cc_start: 0.4388 (mmm) cc_final: 0.3928 (mmt) REVERT: b 250 MET cc_start: 0.1524 (ttt) cc_final: 0.0062 (mtp) REVERT: b 300 MET cc_start: 0.0781 (tpt) cc_final: 0.0389 (tpt) REVERT: b 496 MET cc_start: -0.3315 (tpt) cc_final: -0.3771 (tpt) REVERT: b 712 MET cc_start: 0.4490 (ttm) cc_final: 0.3800 (ttp) REVERT: b 721 MET cc_start: 0.7137 (tpp) cc_final: 0.6395 (tpp) REVERT: A 469 MET cc_start: 0.7786 (tpp) cc_final: 0.7513 (tpp) REVERT: A 1191 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: B 779 ILE cc_start: 0.9111 (mm) cc_final: 0.8495 (tt) REVERT: B 1054 MET cc_start: 0.8003 (mpp) cc_final: 0.7567 (mtm) REVERT: E 208 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8337 (tt) REVERT: F 112 ASP cc_start: 0.6442 (p0) cc_final: 0.6156 (p0) REVERT: H 118 TYR cc_start: 0.7548 (m-80) cc_final: 0.7074 (m-80) REVERT: Z 460 MET cc_start: 0.3983 (tpp) cc_final: 0.3610 (tpp) outliers start: 92 outliers final: 81 residues processed: 455 average time/residue: 0.5845 time to fit residues: 449.0251 Evaluate side-chains 440 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 357 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain b residue 182 MET Chi-restraints excluded: chain b residue 362 MET Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain b residue 634 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 329 optimal weight: 0.0970 chunk 529 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 368 optimal weight: 4.9990 chunk 555 optimal weight: 9.9990 chunk 511 optimal weight: 4.9990 chunk 442 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 HIS ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN B1049 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 47793 Z= 0.213 Angle : 0.722 25.347 64976 Z= 0.353 Chirality : 0.045 0.403 7206 Planarity : 0.004 0.104 8075 Dihedral : 14.406 179.368 7202 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 1.95 % Allowed : 18.36 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 5529 helix: 1.11 (0.13), residues: 1785 sheet: -0.78 (0.17), residues: 870 loop : -0.46 (0.12), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1192 HIS 0.011 0.001 HIS A 465 PHE 0.018 0.001 PHE G 44 TYR 0.038 0.001 TYR K 61 ARG 0.007 0.000 ARG A1167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11058 Ramachandran restraints generated. 5529 Oldfield, 0 Emsley, 5529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 362 time to evaluate : 5.250 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: a 61 MET cc_start: -0.2032 (mtt) cc_final: -0.2526 (mpp) REVERT: a 276 MET cc_start: -0.1567 (mtt) cc_final: -0.2061 (mpp) REVERT: a 437 MET cc_start: -0.0023 (ptp) cc_final: -0.2276 (ttt) REVERT: b 171 MET cc_start: -0.4466 (mmt) cc_final: -0.4950 (mmp) REVERT: b 175 MET cc_start: 0.4513 (mmm) cc_final: 0.4013 (mmt) REVERT: b 250 MET cc_start: 0.1538 (ttt) cc_final: 0.0058 (mtp) REVERT: b 300 MET cc_start: 0.0812 (tpt) cc_final: 0.0399 (tpt) REVERT: b 496 MET cc_start: -0.3294 (tpt) cc_final: -0.3743 (tpt) REVERT: b 712 MET cc_start: 0.4437 (ttm) cc_final: 0.3789 (ttp) REVERT: b 721 MET cc_start: 0.7124 (tpp) cc_final: 0.6843 (tpp) REVERT: A 469 MET cc_start: 0.7795 (tpp) cc_final: 0.7486 (tpp) REVERT: B 702 MET cc_start: 0.7734 (tpp) cc_final: 0.6888 (tpp) REVERT: B 719 SER cc_start: 0.7952 (OUTLIER) cc_final: 0.7618 (m) REVERT: B 779 ILE cc_start: 0.9112 (mm) cc_final: 0.8513 (tt) REVERT: B 933 ASP cc_start: 0.7359 (m-30) cc_final: 0.6969 (m-30) REVERT: B 1054 MET cc_start: 0.7963 (mpp) cc_final: 0.7554 (mtm) REVERT: E 208 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8360 (tt) REVERT: F 112 ASP cc_start: 0.6471 (p0) cc_final: 0.6158 (p0) REVERT: G 164 MET cc_start: 0.6938 (mmm) cc_final: 0.6707 (mmm) REVERT: L 44 MET cc_start: 0.6355 (mmm) cc_final: 0.5901 (mmp) REVERT: Z 460 MET cc_start: 0.3805 (tpp) cc_final: 0.3555 (tpp) outliers start: 94 outliers final: 83 residues processed: 438 average time/residue: 0.5954 time to fit residues: 443.3601 Evaluate side-chains 434 residues out of total 4956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 5.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 239 LYS Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 356 VAL Chi-restraints excluded: chain a residue 362 TYR Chi-restraints excluded: chain a residue 416 PHE Chi-restraints excluded: chain b residue 182 MET Chi-restraints excluded: chain b residue 362 MET Chi-restraints excluded: chain b residue 426 ARG Chi-restraints excluded: chain b residue 546 ARG Chi-restraints excluded: chain b residue 634 ASP Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 618 TYR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1184 THR Chi-restraints excluded: chain A residue 1191 GLU Chi-restraints excluded: chain A residue 1197 TYR Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 900 GLU Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 119 CYS Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain Z residue 743 ILE Chi-restraints excluded: chain Z residue 750 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 558 random chunks: chunk 351 optimal weight: 4.9990 chunk 471 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 408 optimal weight: 0.9980 chunk 65 optimal weight: 40.0000 chunk 123 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 403 GLN A 412 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN A 884 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN ** B 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 ASN ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.097464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061284 restraints weight = 299597.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.061989 restraints weight = 146954.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062361 restraints weight = 90659.631| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 47793 Z= 0.454 Angle : 0.819 13.684 64976 Z= 0.413 Chirality : 0.047 0.375 7206 Planarity : 0.005 0.103 8075 Dihedral : 14.445 177.034 7201 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 2.26 % Allowed : 18.09 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5529 helix: 0.83 (0.12), residues: 1794 sheet: -0.98 (0.17), residues: 872 loop : -0.59 (0.12), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1192 HIS 0.011 0.002 HIS A 465 PHE 0.023 0.002 PHE G 44 TYR 0.040 0.002 TYR B 752 ARG 0.032 0.001 ARG B1080 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10639.36 seconds wall clock time: 198 minutes 29.32 seconds (11909.32 seconds total)