Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 03:51:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/04_2023/6hiz_0233_neut_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 149 5.49 5 Mg 3 5.21 5 S 328 5.16 5 C 47969 2.51 5 N 13956 2.21 5 O 14440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "DB GLU 131": "OE1" <-> "OE2" Residue "DB GLU 350": "OE1" <-> "OE2" Residue "DB ARG 383": "NH1" <-> "NH2" Residue "DB GLU 554": "OE1" <-> "OE2" Residue "DB GLU 584": "OE1" <-> "OE2" Residue "DB GLU 597": "OE1" <-> "OE2" Residue "DB ARG 879": "NH1" <-> "NH2" Residue "DB GLU 890": "OE1" <-> "OE2" Residue "DC PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 171": "OE1" <-> "OE2" Residue "DC GLU 272": "OE1" <-> "OE2" Residue "DC GLU 355": "OE1" <-> "OE2" Residue "DC ARG 535": "NH1" <-> "NH2" Residue "DC GLU 581": "OE1" <-> "OE2" Residue "DC GLU 747": "OE1" <-> "OE2" Residue "DC ARG 786": "NH1" <-> "NH2" Residue "DC TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 946": "OE1" <-> "OE2" Residue "DC GLU 952": "OE1" <-> "OE2" Residue "DC GLU 1075": "OE1" <-> "OE2" Residue "DE GLU 185": "OE1" <-> "OE2" Residue "DE ARG 447": "NH1" <-> "NH2" Residue "DE GLU 570": "OE1" <-> "OE2" Residue "DE GLU 630": "OE1" <-> "OE2" Residue "DE ARG 710": "NH1" <-> "NH2" Residue "DF ARG 55": "NH1" <-> "NH2" Residue "DF TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DF PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DF ASP 258": "OD1" <-> "OD2" Residue "DF GLU 269": "OE1" <-> "OE2" Residue "DF ARG 284": "NH1" <-> "NH2" Residue "DF GLU 307": "OE1" <-> "OE2" Residue "DF GLU 332": "OE1" <-> "OE2" Residue "DF GLU 342": "OE1" <-> "OE2" Residue "DF GLU 343": "OE1" <-> "OE2" Residue "DF GLU 344": "OE1" <-> "OE2" Residue "DF GLU 394": "OE1" <-> "OE2" Residue "DF ARG 397": "NH1" <-> "NH2" Residue "DF ARG 535": "NH1" <-> "NH2" Residue "DF GLU 579": "OE1" <-> "OE2" Residue "DG ARG 111": "NH1" <-> "NH2" Residue "DG ARG 213": "NH1" <-> "NH2" Residue "DG ARG 309": "NH1" <-> "NH2" Residue "DG GLU 471": "OE1" <-> "OE2" Residue "DG PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DH ARG 51": "NH1" <-> "NH2" Residue "DH ARG 80": "NH1" <-> "NH2" Residue "DH GLU 83": "OE1" <-> "OE2" Residue "DH GLU 167": "OE1" <-> "OE2" Residue "DH TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DH GLU 260": "OE1" <-> "OE2" Residue "DH GLU 262": "OE1" <-> "OE2" Residue "DH PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DH GLU 318": "OE1" <-> "OE2" Residue "DH ARG 364": "NH1" <-> "NH2" Residue "DH GLU 451": "OE1" <-> "OE2" Residue "DJ TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DJ ARG 63": "NH1" <-> "NH2" Residue "DJ PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DJ GLU 222": "OE1" <-> "OE2" Residue "DT GLU 36": "OE1" <-> "OE2" Residue "DT ARG 52": "NH1" <-> "NH2" Residue "DT GLU 217": "OE1" <-> "OE2" Residue "DT GLU 235": "OE1" <-> "OE2" Residue "DT GLU 236": "OE1" <-> "OE2" Residue "DW GLU 54": "OE1" <-> "OE2" Residue "DX GLU 51": "OE1" <-> "OE2" Residue "DX GLU 91": "OE1" <-> "OE2" Residue "DX GLU 104": "OE1" <-> "OE2" Residue "DY GLU 36": "OE1" <-> "OE2" Residue "DY ARG 87": "NH1" <-> "NH2" Residue "DY ARG 148": "NH1" <-> "NH2" Residue "DY ARG 161": "NH1" <-> "NH2" Residue "CI GLU 56": "OE1" <-> "OE2" Residue "CI GLU 58": "OE1" <-> "OE2" Residue "CI ARG 59": "NH1" <-> "NH2" Residue "CI GLU 352": "OE1" <-> "OE2" Residue "CJ GLU 149": "OE1" <-> "OE2" Residue "CJ GLU 169": "OE1" <-> "OE2" Residue "CJ GLU 278": "OE1" <-> "OE2" Residue "CJ GLU 318": "OE1" <-> "OE2" Residue "CJ GLU 386": "OE1" <-> "OE2" Residue "CJ GLU 557": "OE1" <-> "OE2" Residue "CJ GLU 616": "OE1" <-> "OE2" Residue "CJ ARG 655": "NH1" <-> "NH2" Residue "CJ GLU 794": "OE1" <-> "OE2" Residue "CN PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR GLU 246": "OE1" <-> "OE2" Residue "CR ARG 276": "NH1" <-> "NH2" Residue "Cg GLU 237": "OE1" <-> "OE2" Residue "Cg GLU 272": "OE1" <-> "OE2" Residue "Cg GLU 275": "OE1" <-> "OE2" Residue "Cg GLU 384": "OE1" <-> "OE2" Residue "Cg GLU 406": "OE1" <-> "OE2" Residue "Ci GLU 100": "OE1" <-> "OE2" Residue "Ck GLU 86": "OE1" <-> "OE2" Residue "Ck GLU 103": "OE1" <-> "OE2" Residue "Ck GLU 119": "OE1" <-> "OE2" Residue "Ck ARG 244": "NH1" <-> "NH2" Residue "Ck GLU 340": "OE1" <-> "OE2" Residue "Ck GLU 349": "OE1" <-> "OE2" Residue "Ck ARG 687": "NH1" <-> "NH2" Residue "Ck GLU 730": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 76845 Number of models: 1 Model: "" Number of chains: 33 Chain: "DA" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 993 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "DL" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1153 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 12, 'TRANS': 130} Chain breaks: 1 Chain: "DB" Number of atoms: 9148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9148 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 1052} Chain: "DC" Number of atoms: 8748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8748 Classifications: {'peptide': 1095} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1042} Chain breaks: 3 Chain: "DE" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4831 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 41, 'TRANS': 548} Chain breaks: 6 Chain: "DF" Number of atoms: 4747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4747 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 30, 'TRANS': 559} Chain breaks: 1 Chain: "DG" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4575 Classifications: {'peptide': 566} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 24, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "DH" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4578 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 536} Chain breaks: 1 Chain: "DJ" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2572 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 19, 'TRANS': 295} Chain: "DK" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2007 Classifications: {'peptide': 255} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 246} Chain breaks: 2 Chain: "DT" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2058 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 16, 'TRANS': 222} Chain: "DV" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1346 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 13, 'TRANS': 146} Chain: "DW" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1359 Classifications: {'peptide': 161} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 142} Chain: "DX" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1196 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 132} Chain: "DY" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1293 Classifications: {'peptide': 154} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 140} Chain: "CC" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 646 Classifications: {'peptide': 74} Link IDs: {'TRANS': 73} Chain: "CI" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1754 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "CJ" Number of atoms: 6516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6516 Classifications: {'peptide': 800} Link IDs: {'PCIS': 5, 'PTRANS': 57, 'TRANS': 737} Chain breaks: 1 Chain: "CK" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "CN" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1322 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 4, 'TRANS': 152} Chain: "CR" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 4, 'TRANS': 39} Chain: "CS" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1175 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 132} Chain: "Cg" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3904 Classifications: {'peptide': 482} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 446} Chain: "Ci" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1348 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 15, 'TRANS': 149} Chain: "Ck" Number of atoms: 5596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5596 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 26, 'TRANS': 676} Chain breaks: 1 Chain: "CA" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 3030 Classifications: {'RNA': 143} Modifications used: {'rna2p_pur': 48, 'rna2p_pyr': 35, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 83, 'rna3p': 59} Chain: "UO" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 30 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "UP" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 42 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "DL" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Chain: "DJ" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'UTP': 1} Classifications: {'undetermined': 1} Chain: "Cg" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CA" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'SPD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Cg" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 29.56, per 1000 atoms: 0.38 Number of scatterers: 76845 At special positions: 0 Unit cell: (211.28, 257.15, 187.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 328 16.00 P 149 15.00 Mg 3 11.99 O 14440 8.00 N 13956 7.00 C 47969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.67 Conformation dependent library (CDL) restraints added in 8.7 seconds 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 404 helices and 35 sheets defined 46.6% alpha, 4.1% beta 5 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 20.12 Creating SS restraints... Processing helix chain 'DA' and resid 1190 through 1199 Processing helix chain 'DA' and resid 1203 through 1205 No H-bonds generated for 'chain 'DA' and resid 1203 through 1205' Processing helix chain 'DA' and resid 1210 through 1230 Processing helix chain 'DA' and resid 1238 through 1249 Processing helix chain 'DA' and resid 1265 through 1274 Processing helix chain 'DA' and resid 1279 through 1289 removed outlier: 3.510A pdb=" N VALDA1284 " --> pdb=" O GLUDA1280 " (cutoff:3.500A) Processing helix chain 'DA' and resid 1306 through 1311 Processing helix chain 'DL' and resid 31 through 37 Processing helix chain 'DL' and resid 55 through 62 Processing helix chain 'DL' and resid 71 through 78 Processing helix chain 'DL' and resid 83 through 95 removed outlier: 3.725A pdb=" N LEUDL 88 " --> pdb=" O GLUDL 84 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLYDL 94 " --> pdb=" O GLUDL 90 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALADL 95 " --> pdb=" O PHEDL 91 " (cutoff:3.500A) Processing helix chain 'DL' and resid 103 through 115 Processing helix chain 'DB' and resid 72 through 81 Processing helix chain 'DB' and resid 126 through 159 removed outlier: 4.781A pdb=" N HISDB 141 " --> pdb=" O VALDB 137 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASPDB 142 " --> pdb=" O TRPDB 138 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLNDB 152 " --> pdb=" O GLUDB 148 " (cutoff:3.500A) Processing helix chain 'DB' and resid 163 through 176 Processing helix chain 'DB' and resid 180 through 182 No H-bonds generated for 'chain 'DB' and resid 180 through 182' Processing helix chain 'DB' and resid 191 through 198 Processing helix chain 'DB' and resid 203 through 209 removed outlier: 3.781A pdb=" N GLNDB 208 " --> pdb=" O SERDB 204 " (cutoff:3.500A) Processing helix chain 'DB' and resid 214 through 218 Processing helix chain 'DB' and resid 232 through 258 Processing helix chain 'DB' and resid 261 through 274 removed outlier: 3.968A pdb=" N ARGDB 274 " --> pdb=" O THRDB 270 " (cutoff:3.500A) Processing helix chain 'DB' and resid 285 through 293 Processing helix chain 'DB' and resid 311 through 324 removed outlier: 3.659A pdb=" N SERDB 322 " --> pdb=" O LEUDB 318 " (cutoff:3.500A) Processing helix chain 'DB' and resid 328 through 342 removed outlier: 4.255A pdb=" N VALDB 342 " --> pdb=" O ALADB 338 " (cutoff:3.500A) Processing helix chain 'DB' and resid 349 through 379 removed outlier: 3.525A pdb=" N GLUDB 354 " --> pdb=" O GLNDB 351 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASNDB 358 " --> pdb=" O GLNDB 355 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALADB 362 " --> pdb=" O ILEDB 359 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHEDB 379 " --> pdb=" O ALADB 376 " (cutoff:3.500A) Processing helix chain 'DB' and resid 405 through 415 Processing helix chain 'DB' and resid 424 through 427 removed outlier: 4.321A pdb=" N TRPDB 427 " --> pdb=" O ASPDB 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'DB' and resid 424 through 427' Processing helix chain 'DB' and resid 429 through 432 No H-bonds generated for 'chain 'DB' and resid 429 through 432' Processing helix chain 'DB' and resid 446 through 457 Processing helix chain 'DB' and resid 464 through 467 Processing helix chain 'DB' and resid 475 through 485 Processing helix chain 'DB' and resid 490 through 492 No H-bonds generated for 'chain 'DB' and resid 490 through 492' Processing helix chain 'DB' and resid 495 through 498 Processing helix chain 'DB' and resid 514 through 516 No H-bonds generated for 'chain 'DB' and resid 514 through 516' Processing helix chain 'DB' and resid 530 through 551 Processing helix chain 'DB' and resid 561 through 577 Processing helix chain 'DB' and resid 596 through 603 Processing helix chain 'DB' and resid 605 through 608 Processing helix chain 'DB' and resid 611 through 619 Processing helix chain 'DB' and resid 647 through 655 Processing helix chain 'DB' and resid 657 through 662 Processing helix chain 'DB' and resid 666 through 669 Processing helix chain 'DB' and resid 686 through 691 removed outlier: 4.783A pdb=" N HISDB 691 " --> pdb=" O GLUDB 687 " (cutoff:3.500A) Processing helix chain 'DB' and resid 694 through 720 Processing helix chain 'DB' and resid 763 through 770 Processing helix chain 'DB' and resid 811 through 815 Processing helix chain 'DB' and resid 828 through 831 Processing helix chain 'DB' and resid 844 through 857 Processing helix chain 'DB' and resid 933 through 935 No H-bonds generated for 'chain 'DB' and resid 933 through 935' Processing helix chain 'DB' and resid 984 through 986 No H-bonds generated for 'chain 'DB' and resid 984 through 986' Processing helix chain 'DB' and resid 997 through 1001 Processing helix chain 'DB' and resid 1005 through 1007 No H-bonds generated for 'chain 'DB' and resid 1005 through 1007' Processing helix chain 'DB' and resid 1013 through 1016 No H-bonds generated for 'chain 'DB' and resid 1013 through 1016' Processing helix chain 'DB' and resid 1045 through 1054 Processing helix chain 'DB' and resid 1059 through 1061 No H-bonds generated for 'chain 'DB' and resid 1059 through 1061' Processing helix chain 'DB' and resid 1074 through 1076 No H-bonds generated for 'chain 'DB' and resid 1074 through 1076' Processing helix chain 'DB' and resid 1079 through 1081 No H-bonds generated for 'chain 'DB' and resid 1079 through 1081' Processing helix chain 'DB' and resid 1090 through 1106 removed outlier: 5.248A pdb=" N ASNDB1094 " --> pdb=" O HISDB1091 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYRDB1102 " --> pdb=" O LEUDB1099 " (cutoff:3.500A) Processing helix chain 'DB' and resid 1109 through 1114 removed outlier: 4.875A pdb=" N LYSDB1114 " --> pdb=" O LYSDB1110 " (cutoff:3.500A) Processing helix chain 'DB' and resid 1118 through 1124 removed outlier: 4.763A pdb=" N HISDB1124 " --> pdb=" O GLUDB1120 " (cutoff:3.500A) Processing helix chain 'DB' and resid 1137 through 1139 No H-bonds generated for 'chain 'DB' and resid 1137 through 1139' Processing helix chain 'DB' and resid 1142 through 1144 No H-bonds generated for 'chain 'DB' and resid 1142 through 1144' Processing helix chain 'DB' and resid 1147 through 1149 No H-bonds generated for 'chain 'DB' and resid 1147 through 1149' Processing helix chain 'DC' and resid 43 through 53 Processing helix chain 'DC' and resid 64 through 73 Processing helix chain 'DC' and resid 109 through 112 Processing helix chain 'DC' and resid 126 through 151 Processing helix chain 'DC' and resid 153 through 157 Processing helix chain 'DC' and resid 171 through 173 No H-bonds generated for 'chain 'DC' and resid 171 through 173' Processing helix chain 'DC' and resid 179 through 181 No H-bonds generated for 'chain 'DC' and resid 179 through 181' Processing helix chain 'DC' and resid 183 through 194 Processing helix chain 'DC' and resid 203 through 212 Processing helix chain 'DC' and resid 215 through 224 Processing helix chain 'DC' and resid 239 through 241 No H-bonds generated for 'chain 'DC' and resid 239 through 241' Processing helix chain 'DC' and resid 245 through 267 removed outlier: 4.067A pdb=" N SERDC 257 " --> pdb=" O GLUDC 253 " (cutoff:3.500A) Processing helix chain 'DC' and resid 269 through 276 removed outlier: 3.787A pdb=" N ASPDC 273 " --> pdb=" O VALDC 269 " (cutoff:3.500A) Processing helix chain 'DC' and resid 283 through 307 removed outlier: 3.739A pdb=" N VALDC 288 " --> pdb=" O LEUDC 284 " (cutoff:3.500A) Proline residue: DC 290 - end of helix removed outlier: 3.679A pdb=" N ASPDC 294 " --> pdb=" O PRODC 290 " (cutoff:3.500A) Processing helix chain 'DC' and resid 317 through 337 Processing helix chain 'DC' and resid 350 through 368 Processing helix chain 'DC' and resid 378 through 385 Processing helix chain 'DC' and resid 387 through 392 Processing helix chain 'DC' and resid 394 through 398 removed outlier: 4.259A pdb=" N THRDC 398 " --> pdb=" O HISDC 395 " (cutoff:3.500A) Processing helix chain 'DC' and resid 400 through 416 removed outlier: 3.535A pdb=" N THRDC 416 " --> pdb=" O LYSDC 412 " (cutoff:3.500A) Processing helix chain 'DC' and resid 419 through 431 Processing helix chain 'DC' and resid 448 through 453 Processing helix chain 'DC' and resid 455 through 459 Processing helix chain 'DC' and resid 482 through 494 Processing helix chain 'DC' and resid 507 through 576 Proline residue: DC 532 - end of helix removed outlier: 3.848A pdb=" N SERDC 536 " --> pdb=" O PRODC 532 " (cutoff:3.500A) Proline residue: DC 557 - end of helix removed outlier: 3.831A pdb=" N ARGDC 575 " --> pdb=" O METDC 571 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEUDC 576 " --> pdb=" O GLUDC 572 " (cutoff:3.500A) Processing helix chain 'DC' and resid 627 through 638 Processing helix chain 'DC' and resid 650 through 662 Processing helix chain 'DC' and resid 675 through 698 Processing helix chain 'DC' and resid 700 through 716 removed outlier: 3.826A pdb=" N GLNDC 707 " --> pdb=" O ALADC 703 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARGDC 715 " --> pdb=" O SERDC 711 " (cutoff:3.500A) Processing helix chain 'DC' and resid 798 through 800 No H-bonds generated for 'chain 'DC' and resid 798 through 800' Processing helix chain 'DC' and resid 819 through 827 Processing helix chain 'DC' and resid 846 through 856 Processing helix chain 'DC' and resid 863 through 871 Processing helix chain 'DC' and resid 881 through 888 Processing helix chain 'DC' and resid 897 through 900 No H-bonds generated for 'chain 'DC' and resid 897 through 900' Processing helix chain 'DC' and resid 904 through 920 Proline residue: DC 911 - end of helix Processing helix chain 'DC' and resid 926 through 943 removed outlier: 4.984A pdb=" N ARGDC 934 " --> pdb=" O ALADC 930 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SERDC 935 " --> pdb=" O THRDC 931 " (cutoff:3.500A) Processing helix chain 'DC' and resid 945 through 948 No H-bonds generated for 'chain 'DC' and resid 945 through 948' Processing helix chain 'DC' and resid 972 through 985 Processing helix chain 'DC' and resid 1030 through 1069 Proline residue: DC1058 - end of helix Processing helix chain 'DC' and resid 1071 through 1073 No H-bonds generated for 'chain 'DC' and resid 1071 through 1073' Processing helix chain 'DC' and resid 1078 through 1100 removed outlier: 4.076A pdb=" N ARGDC1082 " --> pdb=" O LYSDC1079 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALADC1085 " --> pdb=" O ARGDC1082 " (cutoff:3.500A) Processing helix chain 'DC' and resid 1135 through 1137 No H-bonds generated for 'chain 'DC' and resid 1135 through 1137' Processing helix chain 'DE' and resid 46 through 51 removed outlier: 3.611A pdb=" N ARGDE 51 " --> pdb=" O TYRDE 47 " (cutoff:3.500A) Processing helix chain 'DE' and resid 58 through 64 Processing helix chain 'DE' and resid 77 through 103 Processing helix chain 'DE' and resid 155 through 184 Processing helix chain 'DE' and resid 200 through 210 Processing helix chain 'DE' and resid 219 through 234 removed outlier: 3.633A pdb=" N GLUDE 223 " --> pdb=" O ASNDE 219 " (cutoff:3.500A) Processing helix chain 'DE' and resid 236 through 238 No H-bonds generated for 'chain 'DE' and resid 236 through 238' Processing helix chain 'DE' and resid 241 through 251 removed outlier: 4.758A pdb=" N TYRDE 245 " --> pdb=" O SERDE 242 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLUDE 251 " --> pdb=" O THRDE 248 " (cutoff:3.500A) Processing helix chain 'DE' and resid 287 through 300 Processing helix chain 'DE' and resid 305 through 314 Processing helix chain 'DE' and resid 333 through 348 Processing helix chain 'DE' and resid 405 through 410 Processing helix chain 'DE' and resid 412 through 426 Proline residue: DE 416 - end of helix removed outlier: 3.781A pdb=" N PHEDE 426 " --> pdb=" O PHEDE 423 " (cutoff:3.500A) Processing helix chain 'DE' and resid 434 through 437 No H-bonds generated for 'chain 'DE' and resid 434 through 437' Processing helix chain 'DE' and resid 442 through 445 No H-bonds generated for 'chain 'DE' and resid 442 through 445' Processing helix chain 'DE' and resid 463 through 471 Processing helix chain 'DE' and resid 482 through 513 removed outlier: 5.155A pdb=" N ARGDE 502 " --> pdb=" O GLNDE 498 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASPDE 503 " --> pdb=" O LYSDE 499 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILEDE 505 " --> pdb=" O HISDE 501 " (cutoff:3.500A) Processing helix chain 'DE' and resid 540 through 564 removed outlier: 3.517A pdb=" N LEUDE 546 " --> pdb=" O GLUDE 542 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALADE 560 " --> pdb=" O LEUDE 556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THRDE 561 " --> pdb=" O TYRDE 557 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASNDE 562 " --> pdb=" O ASPDE 558 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASPDE 563 " --> pdb=" O SERDE 559 " (cutoff:3.500A) Processing helix chain 'DE' and resid 569 through 577 removed outlier: 3.629A pdb=" N THRDE 577 " --> pdb=" O GLNDE 573 " (cutoff:3.500A) Processing helix chain 'DE' and resid 594 through 601 Processing helix chain 'DE' and resid 605 through 612 Processing helix chain 'DE' and resid 622 through 647 Processing helix chain 'DE' and resid 652 through 682 removed outlier: 3.542A pdb=" N VALDE 657 " --> pdb=" O THRDE 653 " (cutoff:3.500A) Processing helix chain 'DE' and resid 701 through 708 removed outlier: 3.616A pdb=" N LEUDE 708 " --> pdb=" O LEUDE 704 " (cutoff:3.500A) Processing helix chain 'DE' and resid 730 through 737 Processing helix chain 'DF' and resid 16 through 24 removed outlier: 4.256A pdb=" N ILEDF 21 " --> pdb=" O ALADF 17 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYRDF 24 " --> pdb=" O SERDF 20 " (cutoff:3.500A) Processing helix chain 'DF' and resid 44 through 52 Processing helix chain 'DF' and resid 85 through 91 removed outlier: 4.011A pdb=" N LYSDF 90 " --> pdb=" O ARGDF 86 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYRDF 91 " --> pdb=" O GLUDF 87 " (cutoff:3.500A) Processing helix chain 'DF' and resid 99 through 102 Processing helix chain 'DF' and resid 106 through 108 No H-bonds generated for 'chain 'DF' and resid 106 through 108' Processing helix chain 'DF' and resid 160 through 169 Processing helix chain 'DF' and resid 175 through 182 Processing helix chain 'DF' and resid 200 through 211 Processing helix chain 'DF' and resid 215 through 224 removed outlier: 4.398A pdb=" N ARGDF 224 " --> pdb=" O GLUDF 220 " (cutoff:3.500A) Processing helix chain 'DF' and resid 231 through 242 Processing helix chain 'DF' and resid 247 through 257 Processing helix chain 'DF' and resid 268 through 280 Processing helix chain 'DF' and resid 284 through 295 Processing helix chain 'DF' and resid 298 through 301 No H-bonds generated for 'chain 'DF' and resid 298 through 301' Processing helix chain 'DF' and resid 310 through 326 Processing helix chain 'DF' and resid 330 through 342 Processing helix chain 'DF' and resid 348 through 364 Processing helix chain 'DF' and resid 372 through 376 Processing helix chain 'DF' and resid 379 through 411 Proline residue: DF 389 - end of helix removed outlier: 3.992A pdb=" N VALDF 411 " --> pdb=" O ALADF 407 " (cutoff:3.500A) Processing helix chain 'DF' and resid 422 through 424 No H-bonds generated for 'chain 'DF' and resid 422 through 424' Processing helix chain 'DF' and resid 436 through 447 Processing helix chain 'DF' and resid 452 through 458 Processing helix chain 'DF' and resid 472 through 486 Processing helix chain 'DF' and resid 488 through 493 Processing helix chain 'DF' and resid 534 through 537 No H-bonds generated for 'chain 'DF' and resid 534 through 537' Processing helix chain 'DF' and resid 561 through 564 No H-bonds generated for 'chain 'DF' and resid 561 through 564' Processing helix chain 'DF' and resid 581 through 595 Processing helix chain 'DG' and resid 15 through 18 No H-bonds generated for 'chain 'DG' and resid 15 through 18' Processing helix chain 'DG' and resid 20 through 22 No H-bonds generated for 'chain 'DG' and resid 20 through 22' Processing helix chain 'DG' and resid 30 through 37 removed outlier: 4.165A pdb=" N ASPDG 34 " --> pdb=" O SERDG 30 " (cutoff:3.500A) Processing helix chain 'DG' and resid 55 through 60 removed outlier: 3.801A pdb=" N GLNDG 60 " --> pdb=" O ARGDG 56 " (cutoff:3.500A) Processing helix chain 'DG' and resid 63 through 76 removed outlier: 4.101A pdb=" N TYRDG 68 " --> pdb=" O ARGDG 64 " (cutoff:3.500A) Processing helix chain 'DG' and resid 80 through 92 removed outlier: 3.829A pdb=" N LEUDG 85 " --> pdb=" O PRODG 81 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEUDG 86 " --> pdb=" O SERDG 82 " (cutoff:3.500A) Processing helix chain 'DG' and resid 99 through 111 removed outlier: 3.600A pdb=" N ARGDG 108 " --> pdb=" O VALDG 104 " (cutoff:3.500A) Processing helix chain 'DG' and resid 117 through 129 Processing helix chain 'DG' and resid 136 through 147 Processing helix chain 'DG' and resid 154 through 182 Proline residue: DG 181 - end of helix Processing helix chain 'DG' and resid 185 through 200 Processing helix chain 'DG' and resid 208 through 217 removed outlier: 3.612A pdb=" N THRDG 217 " --> pdb=" O ARGDG 213 " (cutoff:3.500A) Processing helix chain 'DG' and resid 221 through 233 Processing helix chain 'DG' and resid 275 through 277 No H-bonds generated for 'chain 'DG' and resid 275 through 277' Processing helix chain 'DG' and resid 280 through 296 removed outlier: 3.649A pdb=" N VALDG 286 " --> pdb=" O ASPDG 282 " (cutoff:3.500A) Processing helix chain 'DG' and resid 307 through 320 Processing helix chain 'DG' and resid 327 through 338 Processing helix chain 'DG' and resid 346 through 359 Processing helix chain 'DG' and resid 368 through 376 Processing helix chain 'DG' and resid 382 through 391 Processing helix chain 'DG' and resid 445 through 462 Processing helix chain 'DG' and resid 475 through 493 Processing helix chain 'DG' and resid 530 through 553 Processing helix chain 'DG' and resid 563 through 584 Processing helix chain 'DG' and resid 594 through 617 Processing helix chain 'DG' and resid 619 through 621 No H-bonds generated for 'chain 'DG' and resid 619 through 621' Processing helix chain 'DG' and resid 624 through 630 Processing helix chain 'DH' and resid 41 through 78 Processing helix chain 'DH' and resid 87 through 100 Processing helix chain 'DH' and resid 103 through 115 Proline residue: DH 108 - end of helix Processing helix chain 'DH' and resid 121 through 132 removed outlier: 3.871A pdb=" N ALADH 125 " --> pdb=" O ALADH 121 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALADH 132 " --> pdb=" O ILEDH 128 " (cutoff:3.500A) Processing helix chain 'DH' and resid 136 through 142 Processing helix chain 'DH' and resid 149 through 158 removed outlier: 3.658A pdb=" N TYRDH 153 " --> pdb=" O PRODH 149 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASPDH 158 " --> pdb=" O LYSDH 154 " (cutoff:3.500A) Processing helix chain 'DH' and resid 161 through 183 Processing helix chain 'DH' and resid 196 through 199 No H-bonds generated for 'chain 'DH' and resid 196 through 199' Processing helix chain 'DH' and resid 201 through 216 removed outlier: 4.378A pdb=" N THRDH 216 " --> pdb=" O ARGDH 212 " (cutoff:3.500A) Processing helix chain 'DH' and resid 219 through 225 Processing helix chain 'DH' and resid 228 through 236 Processing helix chain 'DH' and resid 242 through 254 Processing helix chain 'DH' and resid 258 through 271 Processing helix chain 'DH' and resid 273 through 275 No H-bonds generated for 'chain 'DH' and resid 273 through 275' Processing helix chain 'DH' and resid 278 through 290 Processing helix chain 'DH' and resid 294 through 306 removed outlier: 3.762A pdb=" N TRPDH 301 " --> pdb=" O CYSDH 297 " (cutoff:3.500A) Processing helix chain 'DH' and resid 314 through 329 Processing helix chain 'DH' and resid 334 through 336 No H-bonds generated for 'chain 'DH' and resid 334 through 336' Processing helix chain 'DH' and resid 342 through 359 Proline residue: DH 351 - end of helix removed outlier: 4.094A pdb=" N LEUDH 354 " --> pdb=" O PRODH 351 " (cutoff:3.500A) Processing helix chain 'DH' and resid 369 through 381 Processing helix chain 'DH' and resid 386 through 391 removed outlier: 3.774A pdb=" N GLUDH 391 " --> pdb=" O SERDH 387 " (cutoff:3.500A) Processing helix chain 'DH' and resid 395 through 407 Processing helix chain 'DH' and resid 461 through 464 No H-bonds generated for 'chain 'DH' and resid 461 through 464' Processing helix chain 'DH' and resid 496 through 498 No H-bonds generated for 'chain 'DH' and resid 496 through 498' Processing helix chain 'DH' and resid 506 through 508 No H-bonds generated for 'chain 'DH' and resid 506 through 508' Processing helix chain 'DH' and resid 516 through 519 No H-bonds generated for 'chain 'DH' and resid 516 through 519' Processing helix chain 'DH' and resid 522 through 525 No H-bonds generated for 'chain 'DH' and resid 522 through 525' Processing helix chain 'DH' and resid 532 through 544 removed outlier: 3.749A pdb=" N VALDH 536 " --> pdb=" O ARGDH 532 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLUDH 537 " --> pdb=" O LYSDH 533 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 21 through 24 No H-bonds generated for 'chain 'DJ' and resid 21 through 24' Processing helix chain 'DJ' and resid 75 through 78 No H-bonds generated for 'chain 'DJ' and resid 75 through 78' Processing helix chain 'DJ' and resid 80 through 85 removed outlier: 4.632A pdb=" N LYSDJ 85 " --> pdb=" O PRODJ 81 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 97 through 110 Proline residue: DJ 109 - end of helix Processing helix chain 'DJ' and resid 114 through 131 removed outlier: 3.509A pdb=" N GLNDJ 131 " --> pdb=" O HISDJ 127 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 134 through 142 removed outlier: 4.185A pdb=" N METDJ 137 " --> pdb=" O GLYDJ 134 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLUDJ 138 " --> pdb=" O GLYDJ 135 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARGDJ 142 " --> pdb=" O LEUDJ 139 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 144 through 147 No H-bonds generated for 'chain 'DJ' and resid 144 through 147' Processing helix chain 'DJ' and resid 159 through 171 Processing helix chain 'DJ' and resid 175 through 184 removed outlier: 3.984A pdb=" N PHEDJ 181 " --> pdb=" O ARGDJ 178 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASPDJ 182 " --> pdb=" O ALADJ 179 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 192 through 194 No H-bonds generated for 'chain 'DJ' and resid 192 through 194' Processing helix chain 'DJ' and resid 197 through 210 Processing helix chain 'DJ' and resid 213 through 225 Processing helix chain 'DJ' and resid 235 through 244 removed outlier: 3.573A pdb=" N ALADJ 244 " --> pdb=" O ILEDJ 240 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 248 through 260 removed outlier: 4.609A pdb=" N ASNDJ 260 " --> pdb=" O LYSDJ 256 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 263 through 276 Processing helix chain 'DJ' and resid 279 through 283 removed outlier: 4.229A pdb=" N GLYDJ 282 " --> pdb=" O HISDJ 279 " (cutoff:3.500A) Processing helix chain 'DJ' and resid 292 through 305 Processing helix chain 'DJ' and resid 312 through 315 No H-bonds generated for 'chain 'DJ' and resid 312 through 315' Processing helix chain 'DK' and resid 4 through 27 Processing helix chain 'DK' and resid 56 through 63 removed outlier: 5.342A pdb=" N SERDK 61 " --> pdb=" O ALADK 57 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHEDK 62 " --> pdb=" O VALDK 58 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYRDK 63 " --> pdb=" O TRPDK 59 " (cutoff:3.500A) Processing helix chain 'DK' and resid 101 through 132 Processing helix chain 'DK' and resid 134 through 138 Processing helix chain 'DK' and resid 142 through 146 Processing helix chain 'DK' and resid 157 through 164 removed outlier: 5.330A pdb=" N LEUDK 161 " --> pdb=" O PHEDK 158 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYSDK 162 " --> pdb=" O GLUDK 159 " (cutoff:3.500A) Processing helix chain 'DK' and resid 168 through 174 Processing helix chain 'DK' and resid 178 through 190 Processing helix chain 'DK' and resid 228 through 230 No H-bonds generated for 'chain 'DK' and resid 228 through 230' Processing helix chain 'DK' and resid 238 through 241 No H-bonds generated for 'chain 'DK' and resid 238 through 241' Processing helix chain 'DK' and resid 243 through 249 Proline residue: DK 247 - end of helix Processing helix chain 'DK' and resid 262 through 295 removed outlier: 3.580A pdb=" N GLUDK 272 " --> pdb=" O ALADK 268 " (cutoff:3.500A) Processing helix chain 'DK' and resid 304 through 306 No H-bonds generated for 'chain 'DK' and resid 304 through 306' Processing helix chain 'DT' and resid 29 through 31 No H-bonds generated for 'chain 'DT' and resid 29 through 31' Processing helix chain 'DT' and resid 34 through 37 Processing helix chain 'DT' and resid 48 through 50 No H-bonds generated for 'chain 'DT' and resid 48 through 50' Processing helix chain 'DT' and resid 52 through 60 removed outlier: 5.149A pdb=" N GLNDT 56 " --> pdb=" O GLNDT 53 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N HISDT 59 " --> pdb=" O GLNDT 56 " (cutoff:3.500A) Processing helix chain 'DT' and resid 67 through 75 Processing helix chain 'DT' and resid 90 through 92 No H-bonds generated for 'chain 'DT' and resid 90 through 92' Processing helix chain 'DT' and resid 105 through 113 removed outlier: 5.163A pdb=" N GLUDT 109 " --> pdb=" O ASPDT 106 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEUDT 112 " --> pdb=" O GLUDT 109 " (cutoff:3.500A) Processing helix chain 'DT' and resid 116 through 123 Processing helix chain 'DT' and resid 142 through 153 Processing helix chain 'DT' and resid 165 through 170 Processing helix chain 'DT' and resid 192 through 194 No H-bonds generated for 'chain 'DT' and resid 192 through 194' Processing helix chain 'DT' and resid 214 through 219 Processing helix chain 'DT' and resid 226 through 232 removed outlier: 3.688A pdb=" N ARGDT 232 " --> pdb=" O LEUDT 228 " (cutoff:3.500A) Processing helix chain 'DT' and resid 244 through 246 No H-bonds generated for 'chain 'DT' and resid 244 through 246' Processing helix chain 'DV' and resid 53 through 60 removed outlier: 6.139A pdb=" N THRDV 57 " --> pdb=" O GLYDV 54 " (cutoff:3.500A) Processing helix chain 'DV' and resid 74 through 77 Processing helix chain 'DV' and resid 79 through 100 Processing helix chain 'DV' and resid 111 through 113 No H-bonds generated for 'chain 'DV' and resid 111 through 113' Processing helix chain 'DV' and resid 116 through 118 No H-bonds generated for 'chain 'DV' and resid 116 through 118' Processing helix chain 'DV' and resid 135 through 137 No H-bonds generated for 'chain 'DV' and resid 135 through 137' Processing helix chain 'DV' and resid 154 through 157 No H-bonds generated for 'chain 'DV' and resid 154 through 157' Processing helix chain 'DV' and resid 159 through 161 No H-bonds generated for 'chain 'DV' and resid 159 through 161' Processing helix chain 'DV' and resid 179 through 181 No H-bonds generated for 'chain 'DV' and resid 179 through 181' Processing helix chain 'DW' and resid 33 through 35 No H-bonds generated for 'chain 'DW' and resid 33 through 35' Processing helix chain 'DW' and resid 64 through 79 Processing helix chain 'DW' and resid 84 through 96 Processing helix chain 'DW' and resid 123 through 134 Processing helix chain 'DW' and resid 137 through 139 No H-bonds generated for 'chain 'DW' and resid 137 through 139' Processing helix chain 'DW' and resid 158 through 160 No H-bonds generated for 'chain 'DW' and resid 158 through 160' Processing helix chain 'DW' and resid 162 through 168 removed outlier: 5.248A pdb=" N LYSDW 166 " --> pdb=" O GLUDW 163 " (cutoff:3.500A) Processing helix chain 'DX' and resid 42 through 73 removed outlier: 3.761A pdb=" N ARGDX 59 " --> pdb=" O LEUDX 55 " (cutoff:3.500A) Processing helix chain 'DX' and resid 94 through 101 removed outlier: 4.216A pdb=" N TYRDX 101 " --> pdb=" O LEUDX 98 " (cutoff:3.500A) Processing helix chain 'DX' and resid 104 through 109 Processing helix chain 'DX' and resid 114 through 124 Processing helix chain 'DX' and resid 128 through 133 removed outlier: 3.951A pdb=" N ILEDX 131 " --> pdb=" O GLYDX 128 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THRDX 132 " --> pdb=" O PRODX 129 " (cutoff:3.500A) Processing helix chain 'DX' and resid 140 through 143 No H-bonds generated for 'chain 'DX' and resid 140 through 143' Processing helix chain 'DX' and resid 152 through 156 Processing helix chain 'DY' and resid 21 through 30 removed outlier: 3.772A pdb=" N THRDY 27 " --> pdb=" O SERDY 23 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLYDY 28 " --> pdb=" O VALDY 24 " (cutoff:3.500A) Proline residue: DY 29 - end of helix Processing helix chain 'DY' and resid 35 through 48 Processing helix chain 'DY' and resid 53 through 67 Processing helix chain 'DY' and resid 83 through 116 Processing helix chain 'CC' and resid 26 through 28 No H-bonds generated for 'chain 'CC' and resid 26 through 28' Processing helix chain 'CI' and resid 10 through 24 Processing helix chain 'CI' and resid 34 through 64 removed outlier: 3.992A pdb=" N LEUCI 63 " --> pdb=" O ARGCI 59 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N METCI 64 " --> pdb=" O ILECI 60 " (cutoff:3.500A) Processing helix chain 'CI' and resid 340 through 343 No H-bonds generated for 'chain 'CI' and resid 340 through 343' Processing helix chain 'CI' and resid 348 through 360 removed outlier: 4.479A pdb=" N METCI 353 " --> pdb=" O TRPCI 349 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VALCI 354 " --> pdb=" O LEUCI 350 " (cutoff:3.500A) Proline residue: CI 357 - end of helix Processing helix chain 'CI' and resid 365 through 367 No H-bonds generated for 'chain 'CI' and resid 365 through 367' Processing helix chain 'CI' and resid 385 through 402 Processing helix chain 'CI' and resid 404 through 413 Proline residue: CI 409 - end of helix Processing helix chain 'CJ' and resid 11 through 15 removed outlier: 3.606A pdb=" N ARGCJ 14 " --> pdb=" O TYRCJ 11 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 47 through 51 removed outlier: 3.615A pdb=" N LYSCJ 51 " --> pdb=" O PROCJ 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 47 through 51' Processing helix chain 'CJ' and resid 54 through 57 No H-bonds generated for 'chain 'CJ' and resid 54 through 57' Processing helix chain 'CJ' and resid 67 through 69 No H-bonds generated for 'chain 'CJ' and resid 67 through 69' Processing helix chain 'CJ' and resid 90 through 92 No H-bonds generated for 'chain 'CJ' and resid 90 through 92' Processing helix chain 'CJ' and resid 109 through 122 Processing helix chain 'CJ' and resid 126 through 129 Processing helix chain 'CJ' and resid 134 through 136 No H-bonds generated for 'chain 'CJ' and resid 134 through 136' Processing helix chain 'CJ' and resid 140 through 146 Processing helix chain 'CJ' and resid 159 through 169 Processing helix chain 'CJ' and resid 212 through 224 Processing helix chain 'CJ' and resid 237 through 239 No H-bonds generated for 'chain 'CJ' and resid 237 through 239' Processing helix chain 'CJ' and resid 254 through 288 Processing helix chain 'CJ' and resid 294 through 300 Processing helix chain 'CJ' and resid 316 through 341 Processing helix chain 'CJ' and resid 382 through 387 Processing helix chain 'CJ' and resid 410 through 420 removed outlier: 4.671A pdb=" N ARGCJ 420 " --> pdb=" O METCJ 416 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 458 through 461 Processing helix chain 'CJ' and resid 465 through 468 No H-bonds generated for 'chain 'CJ' and resid 465 through 468' Processing helix chain 'CJ' and resid 489 through 496 Processing helix chain 'CJ' and resid 500 through 506 Processing helix chain 'CJ' and resid 555 through 561 Processing helix chain 'CJ' and resid 566 through 572 Processing helix chain 'CJ' and resid 575 through 579 Processing helix chain 'CJ' and resid 601 through 603 No H-bonds generated for 'chain 'CJ' and resid 601 through 603' Processing helix chain 'CJ' and resid 608 through 611 No H-bonds generated for 'chain 'CJ' and resid 608 through 611' Processing helix chain 'CJ' and resid 624 through 631 Processing helix chain 'CJ' and resid 635 through 642 removed outlier: 3.624A pdb=" N VALCJ 641 " --> pdb=" O ALACJ 637 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 674 through 680 Processing helix chain 'CJ' and resid 682 through 690 removed outlier: 3.678A pdb=" N GLUCJ 689 " --> pdb=" O ILECJ 685 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 703 through 705 No H-bonds generated for 'chain 'CJ' and resid 703 through 705' Processing helix chain 'CJ' and resid 730 through 736 Processing helix chain 'CJ' and resid 775 through 779 Processing helix chain 'CK' and resid 18 through 20 No H-bonds generated for 'chain 'CK' and resid 18 through 20' Processing helix chain 'CK' and resid 30 through 32 No H-bonds generated for 'chain 'CK' and resid 30 through 32' Processing helix chain 'CK' and resid 39 through 60 removed outlier: 4.476A pdb=" N ASNCK 43 " --> pdb=" O GLNCK 39 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HISCK 44 " --> pdb=" O GLNCK 40 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASPCK 60 " --> pdb=" O GLNCK 56 " (cutoff:3.500A) Processing helix chain 'CN' and resid 20 through 50 removed outlier: 4.142A pdb=" N CYSCN 39 " --> pdb=" O PHECN 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TRPCN 40 " --> pdb=" O ARGCN 37 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEUCN 41 " --> pdb=" O ASPCN 38 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILECN 48 " --> pdb=" O CYSCN 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLNCN 50 " --> pdb=" O ALACN 47 " (cutoff:3.500A) Processing helix chain 'CN' and resid 62 through 77 Processing helix chain 'CN' and resid 86 through 88 No H-bonds generated for 'chain 'CN' and resid 86 through 88' Processing helix chain 'CN' and resid 115 through 123 Processing helix chain 'CN' and resid 141 through 159 removed outlier: 8.426A pdb=" N TRPCN 148 " --> pdb=" O LYSCN 144 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLUCN 149 " --> pdb=" O LYSCN 145 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HISCN 150 " --> pdb=" O GLYCN 146 " (cutoff:3.500A) Processing helix chain 'CR' and resid 245 through 250 Processing helix chain 'CS' and resid 37 through 39 No H-bonds generated for 'chain 'CS' and resid 37 through 39' Processing helix chain 'CS' and resid 86 through 88 No H-bonds generated for 'chain 'CS' and resid 86 through 88' Processing helix chain 'CS' and resid 108 through 112 Processing helix chain 'CS' and resid 133 through 135 No H-bonds generated for 'chain 'CS' and resid 133 through 135' Processing helix chain 'CS' and resid 140 through 142 No H-bonds generated for 'chain 'CS' and resid 140 through 142' Processing helix chain 'CS' and resid 158 through 166 Processing helix chain 'Cg' and resid 23 through 26 Processing helix chain 'Cg' and resid 30 through 33 No H-bonds generated for 'chain 'Cg' and resid 30 through 33' Processing helix chain 'Cg' and resid 71 through 73 No H-bonds generated for 'chain 'Cg' and resid 71 through 73' Processing helix chain 'Cg' and resid 82 through 88 Processing helix chain 'Cg' and resid 97 through 100 removed outlier: 3.688A pdb=" N THRCg 100 " --> pdb=" O VALCg 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cg' and resid 97 through 100' Processing helix chain 'Cg' and resid 113 through 138 removed outlier: 4.525A pdb=" N HISCg 127 " --> pdb=" O ASPCg 123 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRPCg 128 " --> pdb=" O LYSCg 124 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N HISCg 129 " --> pdb=" O VALCg 125 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THRCg 130 " --> pdb=" O GLNCg 126 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYSCg 131 " --> pdb=" O HISCg 127 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SERCg 133 " --> pdb=" O HISCg 129 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VALCg 134 " --> pdb=" O THRCg 130 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 155 through 168 Processing helix chain 'Cg' and resid 179 through 183 removed outlier: 3.950A pdb=" N THRCg 183 " --> pdb=" O LYSCg 180 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 201 through 221 removed outlier: 3.551A pdb=" N ALACg 212 " --> pdb=" O LEUCg 208 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALACg 217 " --> pdb=" O VALCg 213 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THRCg 218 " --> pdb=" O ALACg 214 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SERCg 221 " --> pdb=" O ALACg 217 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 243 through 251 Processing helix chain 'Cg' and resid 257 through 273 removed outlier: 3.612A pdb=" N SERCg 263 " --> pdb=" O ILECg 259 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 288 through 291 No H-bonds generated for 'chain 'Cg' and resid 288 through 291' Processing helix chain 'Cg' and resid 302 through 304 No H-bonds generated for 'chain 'Cg' and resid 302 through 304' Processing helix chain 'Cg' and resid 330 through 332 No H-bonds generated for 'chain 'Cg' and resid 330 through 332' Processing helix chain 'Cg' and resid 334 through 344 Processing helix chain 'Cg' and resid 390 through 393 No H-bonds generated for 'chain 'Cg' and resid 390 through 393' Processing helix chain 'Cg' and resid 406 through 422 Processing helix chain 'Cg' and resid 428 through 430 No H-bonds generated for 'chain 'Cg' and resid 428 through 430' Processing helix chain 'Cg' and resid 437 through 448 Processing helix chain 'Cg' and resid 452 through 464 removed outlier: 4.674A pdb=" N LEUCg 463 " --> pdb=" O TYRCg 459 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VALCg 464 " --> pdb=" O HISCg 460 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 470 through 489 Processing helix chain 'Ci' and resid 20 through 22 No H-bonds generated for 'chain 'Ci' and resid 20 through 22' Processing helix chain 'Ci' and resid 30 through 40 Processing helix chain 'Ci' and resid 51 through 53 No H-bonds generated for 'chain 'Ci' and resid 51 through 53' Processing helix chain 'Ci' and resid 58 through 61 No H-bonds generated for 'chain 'Ci' and resid 58 through 61' Processing helix chain 'Ci' and resid 85 through 89 Processing helix chain 'Ci' and resid 98 through 105 Processing helix chain 'Ci' and resid 110 through 114 Processing helix chain 'Ci' and resid 117 through 124 Processing helix chain 'Ci' and resid 132 through 144 Processing helix chain 'Ci' and resid 160 through 163 No H-bonds generated for 'chain 'Ci' and resid 160 through 163' Processing helix chain 'Ck' and resid 34 through 37 No H-bonds generated for 'chain 'Ck' and resid 34 through 37' Processing helix chain 'Ck' and resid 117 through 121 Processing helix chain 'Ck' and resid 130 through 133 No H-bonds generated for 'chain 'Ck' and resid 130 through 133' Processing helix chain 'Ck' and resid 140 through 146 Processing helix chain 'Ck' and resid 158 through 166 removed outlier: 3.886A pdb=" N LEUCk 164 " --> pdb=" O ALACk 160 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SERCk 165 " --> pdb=" O GLUCk 161 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 170 through 174 Processing helix chain 'Ck' and resid 179 through 202 removed outlier: 3.520A pdb=" N THRCk 201 " --> pdb=" O GLUCk 197 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 207 through 226 Processing helix chain 'Ck' and resid 234 through 256 Processing helix chain 'Ck' and resid 259 through 262 No H-bonds generated for 'chain 'Ck' and resid 259 through 262' Processing helix chain 'Ck' and resid 269 through 284 removed outlier: 5.855A pdb=" N SERCk 273 " --> pdb=" O TYRCk 270 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VALCk 274 " --> pdb=" O GLYCk 271 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VALCk 277 " --> pdb=" O VALCk 274 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 286 through 289 No H-bonds generated for 'chain 'Ck' and resid 286 through 289' Processing helix chain 'Ck' and resid 297 through 308 Processing helix chain 'Ck' and resid 319 through 336 removed outlier: 3.973A pdb=" N ARGCk 335 " --> pdb=" O ARGCk 331 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 369 through 386 Processing helix chain 'Ck' and resid 393 through 398 removed outlier: 3.531A pdb=" N GLUCk 398 " --> pdb=" O ASNCk 394 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 402 through 420 removed outlier: 3.769A pdb=" N LYSCk 418 " --> pdb=" O METCk 414 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 539 through 552 Processing helix chain 'Ck' and resid 558 through 566 Processing helix chain 'Ck' and resid 573 through 585 removed outlier: 4.238A pdb=" N ALACk 578 " --> pdb=" O GLUCk 574 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THRCk 582 " --> pdb=" O ALACk 578 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASNCk 584 " --> pdb=" O ALACk 580 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N METCk 585 " --> pdb=" O ALACk 581 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 595 through 608 Processing helix chain 'Ck' and resid 610 through 614 Processing helix chain 'Ck' and resid 627 through 640 Processing helix chain 'Ck' and resid 644 through 654 removed outlier: 3.767A pdb=" N SERCk 654 " --> pdb=" O ILECk 650 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 689 through 701 removed outlier: 4.730A pdb=" N TRPCk 693 " --> pdb=" O ASPCk 689 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 711 through 714 No H-bonds generated for 'chain 'Ck' and resid 711 through 714' Processing helix chain 'Ck' and resid 727 through 736 Processing helix chain 'Ck' and resid 756 through 778 removed outlier: 4.006A pdb=" N LYSCk 776 " --> pdb=" O ALACk 772 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALACk 777 " --> pdb=" O ASPCk 773 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLNCk 778 " --> pdb=" O ALACk 774 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 781 through 783 No H-bonds generated for 'chain 'Ck' and resid 781 through 783' Processing helix chain 'Ck' and resid 796 through 803 removed outlier: 4.181A pdb=" N HISCk 801 " --> pdb=" O GLNCk 797 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYRCk 802 " --> pdb=" O SERCk 798 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SERCk 803 " --> pdb=" O LYSCk 799 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 807 through 827 removed outlier: 3.736A pdb=" N GLUCk 816 " --> pdb=" O LYSCk 812 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYSCk 826 " --> pdb=" O ARGCk 822 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARGCk 827 " --> pdb=" O ASPCk 823 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 833 through 835 No H-bonds generated for 'chain 'Ck' and resid 833 through 835' Processing sheet with id= A, first strand: chain 'DA' and resid 1262 through 1264 Processing sheet with id= B, first strand: chain 'DB' and resid 95 through 98 Processing sheet with id= C, first strand: chain 'DB' and resid 723 through 725 removed outlier: 6.523A pdb=" N THRDB 798 " --> pdb=" O VALDB 735 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N HISDB 737 " --> pdb=" O PRODB 796 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'DB' and resid 791 through 795 Processing sheet with id= E, first strand: chain 'DB' and resid 746 through 748 Processing sheet with id= F, first strand: chain 'DB' and resid 862 through 865 Processing sheet with id= G, first strand: chain 'DB' and resid 877 through 881 removed outlier: 7.002A pdb=" N LYSDB 919 " --> pdb=" O ILEDB 903 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'DB' and resid 965 through 967 Processing sheet with id= I, first strand: chain 'DB' and resid 1150 through 1153 removed outlier: 6.243A pdb=" N ASPDB1153 " --> pdb=" O VALDB1159 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VALDB1159 " --> pdb=" O ASPDB1153 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'DC' and resid 464 through 466 Processing sheet with id= K, first strand: chain 'DC' and resid 583 through 586 Processing sheet with id= L, first strand: chain 'DC' and resid 611 through 613 removed outlier: 6.050A pdb=" N GLNDC 814 " --> pdb=" O TRPDC 612 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLUDC 784 " --> pdb=" O ARGDC 672 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLUDC 747 " --> pdb=" O VALDC 673 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'DC' and resid 788 through 791 Processing sheet with id= N, first strand: chain 'DC' and resid 988 through 993 removed outlier: 3.729A pdb=" N SERDC1001 " --> pdb=" O ASPDC1018 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'DC' and resid 667 through 669 removed outlier: 6.793A pdb=" N LEUDC 669 " --> pdb=" O LEUDC 753 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEUDC 753 " --> pdb=" O LEUDC 669 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'DE' and resid 147 through 149 Processing sheet with id= Q, first strand: chain 'DF' and resid 72 through 75 Processing sheet with id= R, first strand: chain 'DF' and resid 504 through 506 removed outlier: 6.229A pdb=" N ARGDF 548 " --> pdb=" O ARGDF 516 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALADF 518 " --> pdb=" O ARGDF 548 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VALDF 550 " --> pdb=" O ALADF 518 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'DG' and resid 242 through 245 Processing sheet with id= T, first strand: chain 'DH' and resid 465 through 471 Processing sheet with id= U, first strand: chain 'DK' and resid 30 through 34 removed outlier: 6.323A pdb=" N SERDK 43 " --> pdb=" O VALDK 48 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VALDK 48 " --> pdb=" O SERDK 43 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'DT' and resid 100 through 102 removed outlier: 8.782A pdb=" N LEUDT 101 " --> pdb=" O THRDT 81 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILEDT 83 " --> pdb=" O LEUDT 101 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASPDT 133 " --> pdb=" O HISDT 82 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILEDT 84 " --> pdb=" O ASPDT 133 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILEDT 135 " --> pdb=" O ILEDT 84 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HISDT 158 " --> pdb=" O VALDT 134 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEUDT 136 " --> pdb=" O HISDT 158 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYRDT 160 " --> pdb=" O LEUDT 136 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'CC' and resid 50 through 54 Processing sheet with id= X, first strand: chain 'CI' and resid 305 through 312 removed outlier: 6.156A pdb=" N ILECI 332 " --> pdb=" O ALACI 370 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILECI 372 " --> pdb=" O ILECI 332 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THRCI 334 " --> pdb=" O ILECI 372 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N SERCI 374 " --> pdb=" O THRCI 334 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'CJ' and resid 70 through 72 Processing sheet with id= Z, first strand: chain 'CJ' and resid 428 through 435 removed outlier: 4.280A pdb=" N PHECJ 398 " --> pdb=" O LEUCJ 364 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'CJ' and resid 367 through 374 Processing sheet with id= AB, first strand: chain 'CJ' and resid 480 through 482 Processing sheet with id= AC, first strand: chain 'CJ' and resid 538 through 540 Processing sheet with id= AD, first strand: chain 'CJ' and resid 615 through 617 Processing sheet with id= AE, first strand: chain 'CS' and resid 117 through 119 removed outlier: 4.426A pdb=" N VALCS 117 " --> pdb=" O PHECS 128 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Cg' and resid 39 through 42 removed outlier: 3.633A pdb=" N THRCg 53 " --> pdb=" O THRCg 42 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Cg' and resid 77 through 80 removed outlier: 4.301A pdb=" N ARGCg 107 " --> pdb=" O VALCg 80 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Cg' and resid 397 through 400 removed outlier: 6.561A pdb=" N VALCg 281 " --> pdb=" O PHECg 352 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILECg 354 " --> pdb=" O VALCg 281 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILECg 283 " --> pdb=" O ILECg 354 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N CYSCg 356 " --> pdb=" O ILECg 283 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VALCg 285 " --> pdb=" O CYSCg 356 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VALCg 172 " --> pdb=" O VALCg 282 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VALCg 284 " --> pdb=" O VALCg 172 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEUCg 174 " --> pdb=" O VALCg 284 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Ck' and resid 673 through 675 2727 hydrogen bonds defined for protein. 7533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 27.32 Time building geometry restraints manager: 28.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 13957 1.32 - 1.46: 27822 1.46 - 1.60: 36564 1.60 - 1.74: 159 1.74 - 1.88: 550 Bond restraints: 79052 Sorted by residual: bond pdb=" CG HISCJ 424 " pdb=" CD2 HISCJ 424 " ideal model delta sigma weight residual 1.354 1.214 0.140 1.10e-02 8.26e+03 1.63e+02 bond pdb=" C1' UTPDJ 401 " pdb=" C2' UTPDJ 401 " ideal model delta sigma weight residual 1.353 1.570 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" CD2 HISCJ 424 " pdb=" NE2 HISCJ 424 " ideal model delta sigma weight residual 1.374 1.474 -0.100 1.10e-02 8.26e+03 8.20e+01 bond pdb=" CG HISCJ 424 " pdb=" ND1 HISCJ 424 " ideal model delta sigma weight residual 1.378 1.465 -0.087 1.10e-02 8.26e+03 6.21e+01 bond pdb=" C1' UTPDJ 401 " pdb=" O4' UTPDJ 401 " ideal model delta sigma weight residual 1.605 1.458 0.147 2.00e-02 2.50e+03 5.40e+01 ... (remaining 79047 not shown) Histogram of bond angle deviations from ideal: 93.77 - 103.21: 1253 103.21 - 112.66: 41301 112.66 - 122.11: 49072 122.11 - 131.56: 15873 131.56 - 141.01: 281 Bond angle restraints: 107780 Sorted by residual: angle pdb=" C CYSDH 133 " pdb=" N PRODH 134 " pdb=" CA PRODH 134 " ideal model delta sigma weight residual 119.84 106.13 13.71 1.25e+00 6.40e-01 1.20e+02 angle pdb=" C ASNDE 327 " pdb=" N PRODE 328 " pdb=" CA PRODE 328 " ideal model delta sigma weight residual 120.38 109.11 11.27 1.03e+00 9.43e-01 1.20e+02 angle pdb=" C ILECJ 783 " pdb=" N PROCJ 784 " pdb=" CA PROCJ 784 " ideal model delta sigma weight residual 120.31 130.41 -10.10 9.80e-01 1.04e+00 1.06e+02 angle pdb=" C ARGCg 16 " pdb=" N PROCg 17 " pdb=" CA PROCg 17 " ideal model delta sigma weight residual 120.38 130.33 -9.95 1.03e+00 9.43e-01 9.32e+01 angle pdb=" N ARGCk 687 " pdb=" CA ARGCk 687 " pdb=" C ARGCk 687 " ideal model delta sigma weight residual 113.30 126.04 -12.74 1.34e+00 5.57e-01 9.04e+01 ... (remaining 107775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 44940 34.08 - 68.15: 2350 68.15 - 102.23: 114 102.23 - 136.30: 7 136.30 - 170.38: 2 Dihedral angle restraints: 47413 sinusoidal: 20830 harmonic: 26583 Sorted by residual: dihedral pdb=" CA METDX 127 " pdb=" C METDX 127 " pdb=" N GLYDX 128 " pdb=" CA GLYDX 128 " ideal model delta harmonic sigma weight residual -180.00 -118.11 -61.89 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ALADC 775 " pdb=" C ALADC 775 " pdb=" N ASNDC 776 " pdb=" CA ASNDC 776 " ideal model delta harmonic sigma weight residual 180.00 126.61 53.39 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CD ARGDB 586 " pdb=" NE ARGDB 586 " pdb=" CZ ARGDB 586 " pdb=" NH1 ARGDB 586 " ideal model delta sinusoidal sigma weight residual 0.00 80.71 -80.71 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 47410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 10102 0.088 - 0.176: 1362 0.176 - 0.264: 116 0.264 - 0.352: 8 0.352 - 0.440: 3 Chirality restraints: 11591 Sorted by residual: chirality pdb=" CA ARGCk 687 " pdb=" N ARGCk 687 " pdb=" C ARGCk 687 " pdb=" CB ARGCk 687 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA HISCJ 461 " pdb=" N HISCJ 461 " pdb=" C HISCJ 461 " pdb=" CB HISCJ 461 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA HISDB 944 " pdb=" N HISDB 944 " pdb=" C HISDB 944 " pdb=" CB HISDB 944 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 11588 not shown) Planarity restraints: 13538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UTPDJ 401 " -0.226 2.00e-02 2.50e+03 4.17e-01 3.91e+03 pdb=" C2' UTPDJ 401 " 0.328 2.00e-02 2.50e+03 pdb=" C3' UTPDJ 401 " 0.552 2.00e-02 2.50e+03 pdb=" C4' UTPDJ 401 " -0.470 2.00e-02 2.50e+03 pdb=" C5' UTPDJ 401 " -0.008 2.00e-02 2.50e+03 pdb=" N1 UTPDJ 401 " 0.450 2.00e-02 2.50e+03 pdb=" O2' UTPDJ 401 " -0.710 2.00e-02 2.50e+03 pdb=" O3' UTPDJ 401 " 0.334 2.00e-02 2.50e+03 pdb=" O4' UTPDJ 401 " -0.251 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDB 586 " 1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARGDB 586 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARGDB 586 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARGDB 586 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARGDB 586 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDB 383 " 0.423 9.50e-02 1.11e+02 1.90e-01 2.20e+01 pdb=" NE ARGDB 383 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARGDB 383 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARGDB 383 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDB 383 " 0.015 2.00e-02 2.50e+03 ... (remaining 13535 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 229 2.47 - 3.08: 52616 3.08 - 3.69: 117390 3.69 - 4.29: 183186 4.29 - 4.90: 292186 Nonbonded interactions: 645607 Sorted by model distance: nonbonded pdb=" CD2 HISCJ 484 " pdb=" NH1 ARGCJ 495 " model vdw 1.866 3.340 nonbonded pdb=" O3G GTPCg 501 " pdb="MG MGCg 502 " model vdw 1.957 2.170 nonbonded pdb=" NH2 ARGDY 148 " pdb=" OP2 UCA 517 " model vdw 1.974 2.520 nonbonded pdb=" NH1 ARGDG 196 " pdb=" OH TYRDG 211 " model vdw 1.981 2.520 nonbonded pdb=" NZ LYSDF 216 " pdb=" O SERCJ 472 " model vdw 2.003 2.520 ... (remaining 645602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 11.940 Check model and map are aligned: 0.860 Set scattering table: 0.510 Process input model: 168.420 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 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 : 0.009 0.217 79052 Z= 0.612 Angle : 1.388 16.008 107780 Z= 0.930 Chirality : 0.060 0.440 11591 Planarity : 0.009 0.486 13538 Dihedral : 18.083 170.378 30195 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.65 % Rotamer Outliers : 12.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.07), residues: 8966 helix: -2.35 (0.06), residues: 4194 sheet: -0.90 (0.22), residues: 394 loop : -1.45 (0.08), residues: 4378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2697 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1011 poor density : 1686 time to evaluate : 8.386 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 outliers start: 1011 outliers final: 283 residues processed: 2444 average time/residue: 0.8830 time to fit residues: 3476.7776 Evaluate side-chains 1275 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 992 time to evaluate : 7.013 Switching outliers to nearest non-outliers outliers start: 283 outliers final: 1 residues processed: 283 average time/residue: 0.6185 time to fit residues: 333.4009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 0.8980 chunk 691 optimal weight: 0.9980 chunk 383 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 466 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 714 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 434 optimal weight: 0.7980 chunk 532 optimal weight: 3.9990 chunk 828 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DB 92 HIS DB 122 HIS ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 281 GLN ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 414 GLN DB 461 GLN DB 486 HIS DB 551 HIS DB 562 GLN DB 703 HIS DB 737 HIS DB 748 HIS DB 981 HIS DB1004 GLN DB1051 GLN DB1055 GLN DB1113 GLN DB1124 HIS DC 81 HIS ** DC 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 242 HIS DC 360 HIS DC 445 HIS DC 570 HIS DC 574 GLN DC 657 GLN DC 676 GLN DC 782 GLN DC 797 ASN DC 921 HIS DC 943 HIS DC1110 HIS ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DC1141 GLN ** DC1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 105 ASN DE 194 HIS DE 202 HIS DE 414 ASN DE 442 HIS DE 465 ASN DE 658 ASN ** DF 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 41 ASN DF 110 ASN DF 123 HIS DF 140 HIS DF 175 GLN DF 178 ASN DF 187 ASN DF 198 HIS DF 214 HIS DF 283 HIS DF 351 HIS ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 65 ASN DG 71 ASN DG 143 HIS DG 170 ASN ** DG 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 342 ASN DG 351 GLN DG 476 GLN DG 477 GLN DH 27 GLN DH 28 ASN DH 100 HIS DH 160 ASN DH 490 HIS DH 526 ASN DJ 27 GLN DJ 31 HIS DJ 33 ASN DJ 82 GLN DJ 247 ASN DJ 260 ASN DJ 293 ASN DJ 301 HIS DJ 314 GLN DK 171 GLN DK 175 HIS DK 262 ASN DT 16 HIS DT 45 HIS DT 72 HIS DT 82 HIS DT 113 GLN DT 139 HIS DT 154 GLN ** DT 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 219 GLN DV 31 HIS DV 40 HIS DV 48 HIS DV 71 GLN DV 83 GLN DV 118 GLN DW 23 HIS DW 66 HIS DW 71 GLN DW 99 HIS DW 119 GLN DW 121 HIS DW 154 HIS DW 167 GLN DX 58 HIS DY 10 ASN ** DY 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 8 HIS ** CC 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 2 GLN CI 55 GLN CI 318 HIS CI 346 ASN CJ 42 ASN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 105 ASN CJ 134 GLN ** CJ 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 232 ASN CJ 450 HIS CJ 460 HIS CJ 471 GLN CJ 476 ASN CJ 484 HIS ** CJ 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 755 ASN CJ 761 GLN CJ 769 GLN CJ 786 GLN CJ 792 HIS CK 40 GLN CN 96 HIS ** CN 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 142 HIS CN 153 ASN CN 157 GLN ** CR 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 266 ASN ** CS 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CS 160 GLN Cg 164 HIS Cg 184 HIS Cg 251 HIS Cg 289 ASN Cg 301 HIS Cg 397 HIS Ci 19 HIS Ci 29 GLN Ci 96 ASN Ci 112 ASN Ci 136 HIS ** Ci 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 32 GLN Ck 34 GLN ** Ck 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 95 HIS Ck 97 GLN Ck 110 HIS Ck 134 HIS Ck 264 ASN Ck 385 HIS Ck 543 GLN Ck 644 HIS Ck 666 HIS Ck 679 GLN Ck 728 GLN Total number of N/Q/H flips: 149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 79052 Z= 0.212 Angle : 0.632 20.287 107780 Z= 0.336 Chirality : 0.041 0.271 11591 Planarity : 0.005 0.098 13538 Dihedral : 9.978 171.264 11941 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.08), residues: 8966 helix: 0.28 (0.08), residues: 4220 sheet: -0.37 (0.24), residues: 392 loop : -0.61 (0.09), residues: 4354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1128 time to evaluate : 7.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 83 residues processed: 1250 average time/residue: 0.8495 time to fit residues: 1764.9540 Evaluate side-chains 1004 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 921 time to evaluate : 7.035 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.6306 time to fit residues: 107.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 689 optimal weight: 5.9990 chunk 563 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 829 optimal weight: 6.9990 chunk 896 optimal weight: 0.8980 chunk 738 optimal weight: 0.0010 chunk 822 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 665 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1258 ASN DL 99 GLN DB 153 HIS ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 539 GLN DB 729 GLN DB 958 ASN DB1004 GLN ** DC 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 916 HIS DC 920 HIS ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 105 ASN DE 501 HIS DE 671 ASN DF 520 GLN ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS DG 229 HIS DG 230 ASN DG 342 ASN ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 160 ASN DH 512 ASN DJ 27 GLN DJ 36 GLN DK 175 HIS ** DT 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 51 ASN DW 72 GLN DW 119 GLN CC 34 ASN CI 55 GLN CJ 42 ASN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 621 ASN CJ 711 HIS CJ 804 ASN CK 56 GLN CN 78 GLN CN 133 HIS CN 150 HIS CR 249 GLN CR 267 ASN ** CS 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 380 ASN Cg 397 HIS Ck 34 GLN Ck 54 ASN Ck 134 HIS Ck 543 GLN Ck 589 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 79052 Z= 0.177 Angle : 0.544 17.718 107780 Z= 0.282 Chirality : 0.039 0.234 11591 Planarity : 0.005 0.090 13538 Dihedral : 9.473 176.659 11941 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.04 % 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: 0.58 (0.09), residues: 8966 helix: 1.18 (0.08), residues: 4252 sheet: -0.09 (0.24), residues: 400 loop : -0.30 (0.10), residues: 4314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1029 time to evaluate : 7.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 61 residues processed: 1137 average time/residue: 0.8216 time to fit residues: 1550.2765 Evaluate side-chains 949 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 888 time to evaluate : 7.041 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5916 time to fit residues: 77.6287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 0.0470 chunk 623 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 395 optimal weight: 6.9990 chunk 557 optimal weight: 5.9990 chunk 832 optimal weight: 4.9990 chunk 881 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 789 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DB 152 GLN ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 221 HIS ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 958 ASN DB1004 GLN DC 250 GLN DC 776 ASN ** DC 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC1160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 67 ASN ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 569 GLN DG 143 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 140 ASN ** DT 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 71 GLN DW 72 GLN DW 157 ASN CC 34 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 762 GLN CK 56 GLN CR 266 ASN ** CS 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CS 135 ASN Ci 96 ASN Ck 543 GLN Ck 547 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 79052 Z= 0.210 Angle : 0.530 17.115 107780 Z= 0.271 Chirality : 0.039 0.271 11591 Planarity : 0.004 0.090 13538 Dihedral : 9.281 176.034 11941 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.01 % 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 (0.09), residues: 8966 helix: 1.42 (0.08), residues: 4260 sheet: -0.02 (0.25), residues: 393 loop : -0.20 (0.10), residues: 4313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 914 time to evaluate : 7.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 58 residues processed: 998 average time/residue: 0.8244 time to fit residues: 1362.6224 Evaluate side-chains 900 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 842 time to evaluate : 6.956 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.6501 time to fit residues: 77.6868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 734 optimal weight: 0.8980 chunk 500 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 656 optimal weight: 0.9980 chunk 363 optimal weight: 4.9990 chunk 752 optimal weight: 2.9990 chunk 609 optimal weight: 5.9990 chunk 1 optimal weight: 0.0060 chunk 450 optimal weight: 3.9990 chunk 791 optimal weight: 0.6980 chunk 222 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** DL 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 958 ASN DC 360 HIS ** DC 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DC1160 GLN ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 396 GLN ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS DG 249 GLN ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 160 ASN DH 450 ASN DT 161 ASN DV 51 ASN DW 71 GLN DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 25 HIS CI 55 GLN CI 330 ASN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 441 HIS ** CJ 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 56 GLN CR 266 ASN CS 110 HIS Ci 96 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 79052 Z= 0.162 Angle : 0.497 17.117 107780 Z= 0.254 Chirality : 0.038 0.207 11591 Planarity : 0.004 0.086 13538 Dihedral : 9.134 176.980 11941 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.63 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.01 % 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: 1.02 (0.09), residues: 8966 helix: 1.58 (0.08), residues: 4262 sheet: 0.17 (0.25), residues: 402 loop : -0.12 (0.10), residues: 4302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 914 time to evaluate : 7.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 41 residues processed: 976 average time/residue: 0.8595 time to fit residues: 1392.2217 Evaluate side-chains 897 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 856 time to evaluate : 6.996 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6310 time to fit residues: 57.4556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 296 optimal weight: 1.9990 chunk 793 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 517 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 882 optimal weight: 2.9990 chunk 732 optimal weight: 0.9990 chunk 408 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 463 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 99 GLN ** DL 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 281 GLN ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 503 ASN DB 958 ASN ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 153 HIS ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 123 HIS DH 160 ASN DK 219 GLN ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DY 99 GLN ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 67 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 152 GLN CJ 209 GLN ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 621 ASN CN 157 GLN Ci 96 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 79052 Z= 0.210 Angle : 0.513 17.146 107780 Z= 0.260 Chirality : 0.039 0.231 11591 Planarity : 0.004 0.086 13538 Dihedral : 9.083 176.461 11941 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.01 % 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: 1.07 (0.09), residues: 8966 helix: 1.62 (0.08), residues: 4262 sheet: 0.20 (0.25), residues: 394 loop : -0.10 (0.10), residues: 4310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 882 time to evaluate : 7.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 39 residues processed: 945 average time/residue: 0.8319 time to fit residues: 1304.5877 Evaluate side-chains 879 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 840 time to evaluate : 7.129 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5836 time to fit residues: 52.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 850 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 502 optimal weight: 2.9990 chunk 644 optimal weight: 0.0470 chunk 499 optimal weight: 2.9990 chunk 742 optimal weight: 5.9990 chunk 492 optimal weight: 2.9990 chunk 879 optimal weight: 5.9990 chunk 550 optimal weight: 3.9990 chunk 535 optimal weight: 0.6980 chunk 405 optimal weight: 6.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 47 GLN DL 99 GLN DL 272 HIS ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 426 HIS DB 503 ASN DB 785 ASN DB 958 ASN DC 894 HIS ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 650 HIS ** DF 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 182 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 524 HIS DK 175 HIS DK 219 GLN DT 9 GLN ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN DW 119 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 167 HIS ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 67 ASN CI 12 HIS CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 152 GLN ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 130 HIS CN 157 GLN Ci 96 ASN Ci 125 HIS Ck 385 HIS Ck 723 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 79052 Z= 0.301 Angle : 0.561 17.175 107780 Z= 0.286 Chirality : 0.041 0.205 11591 Planarity : 0.005 0.092 13538 Dihedral : 9.183 175.741 11941 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.35 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.09), residues: 8966 helix: 1.54 (0.08), residues: 4249 sheet: 0.19 (0.26), residues: 386 loop : -0.14 (0.10), residues: 4331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 877 time to evaluate : 7.254 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 40 residues processed: 919 average time/residue: 0.8624 time to fit residues: 1315.0017 Evaluate side-chains 877 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 837 time to evaluate : 7.110 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.6197 time to fit residues: 56.0655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 0.9980 chunk 351 optimal weight: 5.9990 chunk 524 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 558 optimal weight: 4.9990 chunk 598 optimal weight: 1.9990 chunk 434 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 690 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1243 GLN DL 99 GLN ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 414 GLN DB 503 ASN DB1061 GLN ** DC1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 198 HIS DF 446 HIS ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 140 ASN DT 240 GLN ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 67 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 152 GLN ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CN 157 GLN Ci 96 ASN Ck 30 GLN ** Ck 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 79052 Z= 0.181 Angle : 0.511 17.106 107780 Z= 0.259 Chirality : 0.038 0.192 11591 Planarity : 0.004 0.092 13538 Dihedral : 9.072 176.814 11941 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 8966 helix: 1.69 (0.08), residues: 4222 sheet: 0.28 (0.26), residues: 381 loop : -0.07 (0.10), residues: 4363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 877 time to evaluate : 7.164 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 901 average time/residue: 0.8530 time to fit residues: 1268.8455 Evaluate side-chains 847 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 829 time to evaluate : 7.095 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6796 time to fit residues: 32.0345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 3.9990 chunk 842 optimal weight: 8.9990 chunk 768 optimal weight: 0.9990 chunk 819 optimal weight: 0.9980 chunk 841 optimal weight: 0.9980 chunk 493 optimal weight: 0.0980 chunk 356 optimal weight: 0.7980 chunk 643 optimal weight: 0.0980 chunk 251 optimal weight: 5.9990 chunk 740 optimal weight: 5.9990 chunk 774 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 99 GLN ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 503 ASN ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 115 HIS ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 351 GLN DH 498 ASN ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 140 ASN DW 72 GLN DW 119 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DY 147 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 728 GLN CJ 798 GLN CN 157 GLN Ci 96 ASN Ck 79 HIS Ck 543 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 79052 Z= 0.151 Angle : 0.500 17.121 107780 Z= 0.252 Chirality : 0.038 0.181 11591 Planarity : 0.004 0.090 13538 Dihedral : 8.949 177.391 11941 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.65 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8966 helix: 1.77 (0.08), residues: 4220 sheet: 0.39 (0.27), residues: 381 loop : -0.02 (0.10), residues: 4365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 895 time to evaluate : 8.661 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 912 average time/residue: 0.9067 time to fit residues: 1380.5162 Evaluate side-chains 853 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 845 time to evaluate : 7.091 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6777 time to fit residues: 19.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 3.9990 chunk 537 optimal weight: 4.9990 chunk 866 optimal weight: 6.9990 chunk 528 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 602 optimal weight: 0.0060 chunk 908 optimal weight: 6.9990 chunk 836 optimal weight: 0.0270 chunk 723 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 558 optimal weight: 3.9990 overall best weight: 1.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1243 GLN DL 99 GLN ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 503 ASN DC 776 ASN ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DV 175 GLN DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DY 147 ASN CC 48 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 152 GLN CJ 209 GLN ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 755 ASN ** CJ 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ci 96 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 79052 Z= 0.260 Angle : 0.542 17.181 107780 Z= 0.274 Chirality : 0.040 0.189 11591 Planarity : 0.005 0.093 13538 Dihedral : 8.976 176.957 11941 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.35 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.09), residues: 8966 helix: 1.68 (0.08), residues: 4236 sheet: 0.39 (0.26), residues: 381 loop : -0.07 (0.10), residues: 4349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17932 Ramachandran restraints generated. 8966 Oldfield, 0 Emsley, 8966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 841 time to evaluate : 7.100 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 850 average time/residue: 0.8990 time to fit residues: 1266.1893 Evaluate side-chains 836 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 824 time to evaluate : 7.119 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6184 time to fit residues: 23.5724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 0.5980 chunk 574 optimal weight: 2.9990 chunk 770 optimal weight: 0.0980 chunk 221 optimal weight: 0.3980 chunk 667 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 724 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 chunk 744 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 99 GLN ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 503 ASN DE 43 HIS ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DJ 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 251 GLN DV 175 GLN DW 72 GLN DW 119 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DW 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DY 147 ASN CI 55 GLN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 152 GLN CJ 209 GLN ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 755 ASN ** CJ 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ci 96 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.076565 restraints weight = 141350.599| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.72 r_work: 0.2753 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 79052 Z= 0.145 Angle : 0.499 17.094 107780 Z= 0.252 Chirality : 0.037 0.181 11591 Planarity : 0.004 0.087 13538 Dihedral : 8.862 178.215 11941 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8966 helix: 1.77 (0.08), residues: 4229 sheet: 0.44 (0.27), residues: 379 loop : -0.00 (0.10), residues: 4358 =============================================================================== Job complete usr+sys time: 23628.29 seconds wall clock time: 412 minutes 48.10 seconds (24768.10 seconds total)