Starting phenix.real_space_refine on Sun Mar 17 06:37:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_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_0233/03_2024/6hiz_0233_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiz_0233/03_2024/6hiz_0233_neut_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 28.80, per 1000 atoms: 0.37 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: 24.09 Conformation dependent library (CDL) restraints added in 9.9 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: 23.38 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: 24.21 Time building geometry restraints manager: 26.42 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=" N1 UTPDJ 401 " ideal model delta sigma weight residual 1.305 1.532 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C2' UTPDJ 401 " pdb=" C3' UTPDJ 401 " ideal model delta sigma weight residual 1.301 1.516 -0.215 2.00e-02 2.50e+03 1.16e+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 ... (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: 45112 34.08 - 68.15: 2524 68.15 - 102.23: 116 102.23 - 136.30: 7 136.30 - 170.38: 2 Dihedral angle restraints: 47761 sinusoidal: 21178 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 47758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 10461 0.097 - 0.195: 1055 0.195 - 0.292: 71 0.292 - 0.389: 5 0.389 - 0.486: 3 Chirality restraints: 11595 Sorted by residual: chirality pdb=" C2' UTPDJ 401 " pdb=" C1' UTPDJ 401 " pdb=" C3' UTPDJ 401 " pdb=" O2' UTPDJ 401 " both_signs ideal model delta sigma weight residual False -2.41 -2.90 0.49 2.00e-01 2.50e+01 5.91e+00 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 ... (remaining 11592 not shown) Planarity restraints: 13537 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" C THRDL 270 " -0.072 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRODL 271 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRODL 271 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRODL 271 " -0.060 5.00e-02 4.00e+02 ... (remaining 13534 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 9.400 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 162.740 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.210 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.940 ------------------------------------------------------------------------------- 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 0.227 79052 Z= 0.614 Angle : 1.388 16.008 107780 Z= 0.930 Chirality : 0.060 0.486 11595 Planarity : 0.008 0.486 13537 Dihedral : 18.472 170.378 30543 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 % Allowed : 11.32 % Favored : 75.88 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPCN 152 HIS 0.016 0.002 HISCJ 461 PHE 0.040 0.003 PHEDX 71 TYR 0.032 0.003 TYRCK 25 ARG 0.010 0.001 ARGDJ 178 *********************** 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 : 7.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1207 PHE cc_start: 0.8521 (m-80) cc_final: 0.8137 (m-80) REVERT: DA 1236 ILE cc_start: 0.8418 (mt) cc_final: 0.8087 (mp) REVERT: DA 1244 LYS cc_start: 0.8341 (mttt) cc_final: 0.8138 (mttt) REVERT: DA 1292 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7515 (m) REVERT: DL 24 HIS cc_start: 0.8901 (m-70) cc_final: 0.8675 (m170) REVERT: DL 269 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8342 (mtt) REVERT: DL 278 ARG cc_start: 0.8695 (mmt-90) cc_final: 0.8420 (mmt-90) REVERT: DL 289 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8497 (mmm-85) REVERT: DL 305 THR cc_start: 0.9057 (m) cc_final: 0.8836 (p) REVERT: DB 103 TYR cc_start: 0.8966 (m-80) cc_final: 0.8747 (m-80) REVERT: DB 276 VAL cc_start: 0.9122 (p) cc_final: 0.8782 (m) REVERT: DB 285 MET cc_start: 0.9188 (mtp) cc_final: 0.8776 (mtm) REVERT: DB 341 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8522 (m) REVERT: DB 368 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8710 (tt0) REVERT: DB 388 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8703 (t) REVERT: DB 394 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7937 (p0) REVERT: DB 582 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8024 (tt0) REVERT: DB 585 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8459 (tpt) REVERT: DB 635 MET cc_start: 0.8408 (mmp) cc_final: 0.8003 (mmm) REVERT: DB 671 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9165 (m) REVERT: DB 699 MET cc_start: 0.8964 (ttp) cc_final: 0.8761 (ttm) REVERT: DB 830 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9209 (mt) REVERT: DB 969 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8950 (t) REVERT: DB 1001 THR cc_start: 0.9253 (m) cc_final: 0.9016 (p) REVERT: DB 1168 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7824 (t0) REVERT: DC 46 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8579 (ttp80) REVERT: DC 114 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: DC 467 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8733 (m) REVERT: DC 475 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8459 (mt) REVERT: DC 495 THR cc_start: 0.9081 (m) cc_final: 0.8879 (p) REVERT: DC 498 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8320 (pp) REVERT: DC 506 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8186 (p) REVERT: DC 544 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: DC 636 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8017 (mt-10) REVERT: DC 749 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: DC 795 GLU cc_start: 0.8665 (mp0) cc_final: 0.7893 (mp0) REVERT: DC 856 ASP cc_start: 0.8722 (m-30) cc_final: 0.8456 (p0) REVERT: DC 881 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8585 (tpp) REVERT: DC 885 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8292 (mp) REVERT: DC 970 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: DC 987 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (m) REVERT: DC 1128 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8473 (mtp85) REVERT: DC 1161 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8533 (mtpt) REVERT: DE 246 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8590 (tp) REVERT: DE 591 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8900 (mt) REVERT: DE 651 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8367 (p0) REVERT: DE 698 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (pp30) REVERT: DF 15 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7054 (p-80) REVERT: DF 39 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8561 (ptt180) REVERT: DF 92 MET cc_start: 0.9271 (ttm) cc_final: 0.9014 (ttp) REVERT: DF 109 MET cc_start: 0.9363 (mtp) cc_final: 0.8915 (mtp) REVERT: DF 157 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8919 (t) REVERT: DF 182 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8003 (mtm180) REVERT: DF 192 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9124 (mm) REVERT: DF 246 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9234 (mttp) REVERT: DF 275 MET cc_start: 0.9294 (tpp) cc_final: 0.9030 (tpp) REVERT: DF 297 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.8630 (ptm160) REVERT: DF 591 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7616 (t70) REVERT: DG 93 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8299 (ptm160) REVERT: DG 102 MET cc_start: 0.9197 (ttp) cc_final: 0.8984 (ttp) REVERT: DG 111 ARG cc_start: 0.8349 (mmt180) cc_final: 0.7960 (mtt-85) REVERT: DG 127 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9502 (mt) REVERT: DG 147 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.9022 (p) REVERT: DG 175 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8813 (tp30) REVERT: DG 186 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (tpt90) REVERT: DG 471 GLU cc_start: 0.8496 (tp30) cc_final: 0.8054 (pm20) REVERT: DG 494 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8874 (p) REVERT: DG 582 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8975 (p) REVERT: DG 615 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.8879 (p) REVERT: DG 623 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9026 (mtp) REVERT: DG 626 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9191 (mt) REVERT: DH 1 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7361 (tpp) REVERT: DH 81 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6501 (tptp) REVERT: DH 83 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5290 (pm20) REVERT: DH 195 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7576 (p90) REVERT: DH 258 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.9042 (mmp) REVERT: DH 354 LEU cc_start: 0.9685 (OUTLIER) cc_final: 0.9474 (mt) REVERT: DH 364 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8566 (ttm170) REVERT: DH 372 MET cc_start: 0.9222 (tpt) cc_final: 0.8998 (tpt) REVERT: DH 377 ASP cc_start: 0.9117 (t70) cc_final: 0.8827 (t0) REVERT: DH 411 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8892 (mt) REVERT: DH 414 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9290 (mt) REVERT: DH 495 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8457 (p) REVERT: DJ 16 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8060 (p0) REVERT: DJ 46 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8795 (mmp80) REVERT: DJ 137 MET cc_start: 0.9477 (OUTLIER) cc_final: 0.8983 (mmm) REVERT: DJ 187 ASP cc_start: 0.8993 (m-30) cc_final: 0.8785 (m-30) REVERT: DJ 236 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8277 (ttt180) REVERT: DJ 302 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.9025 (t) REVERT: DK 135 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8345 (tpp-160) REVERT: DK 297 SER cc_start: 0.8560 (p) cc_final: 0.8326 (m) REVERT: DV 182 TYR cc_start: 0.8588 (m-80) cc_final: 0.8374 (m-80) REVERT: DW 58 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8945 (mmt-90) REVERT: DW 64 TYR cc_start: 0.9096 (m-80) cc_final: 0.8784 (m-80) REVERT: DW 87 ASN cc_start: 0.9251 (m-40) cc_final: 0.8849 (m-40) REVERT: DW 102 MET cc_start: 0.9171 (tpp) cc_final: 0.8963 (tpp) REVERT: DW 115 ASN cc_start: 0.8507 (m-40) cc_final: 0.7448 (t0) REVERT: DW 118 LYS cc_start: 0.9098 (mttt) cc_final: 0.8857 (mmmt) REVERT: DW 119 GLN cc_start: 0.8865 (tt0) cc_final: 0.8536 (tt0) REVERT: DX 34 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8685 (tttt) REVERT: DX 52 GLU cc_start: 0.8889 (pt0) cc_final: 0.8563 (pt0) REVERT: DX 76 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.9120 (mmp-170) REVERT: DX 103 MET cc_start: 0.9048 (mtp) cc_final: 0.8500 (mtp) REVERT: DX 127 MET cc_start: 0.9311 (mmm) cc_final: 0.9100 (mmm) REVERT: DX 136 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8925 (mmm160) REVERT: DX 138 LYS cc_start: 0.9344 (mttt) cc_final: 0.9111 (mttt) REVERT: DY 43 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9366 (mt) REVERT: DY 52 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9068 (pm20) REVERT: DY 92 ASN cc_start: 0.8953 (t0) cc_final: 0.8750 (t0) REVERT: CC 4 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8473 (ptm) REVERT: CC 59 TYR cc_start: 0.8890 (t80) cc_final: 0.8489 (t80) REVERT: CC 60 SER cc_start: 0.8582 (p) cc_final: 0.8370 (p) REVERT: CI 33 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8621 (p) REVERT: CI 38 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9334 (mt) REVERT: CI 290 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7641 (tt) REVERT: CI 324 ARG cc_start: 0.9445 (OUTLIER) cc_final: 0.8986 (ttt180) REVERT: CI 345 ASP cc_start: 0.9397 (t0) cc_final: 0.9144 (t0) REVERT: CI 372 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9238 (mm) REVERT: CJ 87 TYR cc_start: 0.9104 (m-80) cc_final: 0.8709 (m-80) REVERT: CJ 117 TYR cc_start: 0.9299 (m-10) cc_final: 0.9005 (m-10) REVERT: CJ 273 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.9199 (ttp80) REVERT: CJ 287 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9264 (mt) REVERT: CJ 345 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.8983 (m) REVERT: CJ 349 THR cc_start: 0.8773 (m) cc_final: 0.8569 (m) REVERT: CJ 396 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9105 (mmmt) REVERT: CJ 517 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.9068 (p) REVERT: CJ 714 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9096 (p) REVERT: CJ 731 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9076 (mtm) REVERT: CJ 769 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8553 (mt0) REVERT: CK 15 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8910 (ttt90) REVERT: CK 20 MET cc_start: 0.9016 (mmp) cc_final: 0.8529 (tpt) REVERT: CK 52 ASP cc_start: 0.9411 (m-30) cc_final: 0.8808 (m-30) REVERT: CK 55 THR cc_start: 0.8901 (m) cc_final: 0.8694 (p) REVERT: CN 31 MET cc_start: 0.9304 (mtt) cc_final: 0.8922 (mtm) REVERT: CN 70 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9189 (mttt) REVERT: CN 77 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8662 (m110) REVERT: CN 91 ASN cc_start: 0.9277 (m-40) cc_final: 0.8932 (m-40) REVERT: CN 127 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9248 (tp) REVERT: CN 158 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8776 (ttp-170) REVERT: CN 163 TYR cc_start: 0.9291 (m-80) cc_final: 0.9069 (m-80) REVERT: CR 277 SER cc_start: 0.8734 (p) cc_final: 0.8338 (p) REVERT: CS 45 ARG cc_start: 0.9422 (OUTLIER) cc_final: 0.9203 (mtt-85) REVERT: CS 91 THR cc_start: 0.9429 (m) cc_final: 0.9205 (m) REVERT: CS 103 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8716 (mtm-85) REVERT: CS 140 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8807 (mtt) REVERT: CS 155 MET cc_start: 0.8766 (ttp) cc_final: 0.8056 (ttp) REVERT: Cg 112 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8218 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8262 (p-80) REVERT: Cg 143 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8726 (p) REVERT: Cg 186 GLU cc_start: 0.9214 (mm-30) cc_final: 0.9009 (tp30) REVERT: Cg 224 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8878 (mp) REVERT: Cg 262 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8861 (pp30) REVERT: Cg 308 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8775 (tp) REVERT: Ci 18 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9033 (p) REVERT: Ci 48 LYS cc_start: 0.9245 (mttt) cc_final: 0.8951 (mttt) REVERT: Ci 75 ASP cc_start: 0.9157 (p0) cc_final: 0.8915 (p0) REVERT: Ci 76 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8723 (mtp) REVERT: Ci 82 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.8945 (pm20) REVERT: Ci 89 MET cc_start: 0.9083 (mmp) cc_final: 0.8560 (tpp) REVERT: Ci 105 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8971 (ttp-170) REVERT: Ci 136 HIS cc_start: 0.9230 (OUTLIER) cc_final: 0.8552 (t-90) REVERT: Ci 164 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.7976 (p0) REVERT: Ci 174 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7685 (t0) REVERT: Ck 61 LEU cc_start: 0.8739 (mt) cc_final: 0.8537 (mp) REVERT: Ck 130 MET cc_start: 0.9203 (mmp) cc_final: 0.8979 (mmm) REVERT: Ck 292 ASP cc_start: 0.9129 (m-30) cc_final: 0.8475 (p0) REVERT: Ck 337 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (m) REVERT: Ck 353 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8391 (mtp85) REVERT: Ck 411 CYS cc_start: 0.7679 (t) cc_final: 0.7251 (m) REVERT: Ck 564 LEU cc_start: 0.8810 (mt) cc_final: 0.8434 (mt) REVERT: Ck 585 MET cc_start: 0.8486 (ttp) cc_final: 0.8136 (tpp) REVERT: Ck 652 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8781 (ttp-170) REVERT: Ck 682 ASN cc_start: 0.9484 (OUTLIER) cc_final: 0.9190 (p0) REVERT: Ck 733 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9211 (tp) REVERT: Ck 760 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9299 (m) outliers start: 1011 outliers final: 283 residues processed: 2444 average time/residue: 0.8545 time to fit residues: 3350.2145 Evaluate side-chains 1388 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 998 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1191 ILE Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1240 LEU Chi-restraints excluded: chain DA residue 1253 VAL Chi-restraints excluded: chain DA residue 1263 VAL Chi-restraints excluded: chain DA residue 1292 CYS Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 39 THR Chi-restraints excluded: chain DL residue 68 LEU Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 269 MET Chi-restraints excluded: chain DL residue 270 THR Chi-restraints excluded: chain DL residue 286 THR Chi-restraints excluded: chain DB residue 99 VAL Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 204 SER Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 249 SER Chi-restraints excluded: chain DB residue 321 SER Chi-restraints excluded: chain DB residue 341 THR Chi-restraints excluded: chain DB residue 368 GLU Chi-restraints excluded: chain DB residue 388 VAL Chi-restraints excluded: chain DB residue 394 ASP Chi-restraints excluded: chain DB residue 416 ASN Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 479 VAL Chi-restraints excluded: chain DB residue 511 ARG Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 550 LEU Chi-restraints excluded: chain DB residue 553 LEU Chi-restraints excluded: chain DB residue 585 MET Chi-restraints excluded: chain DB residue 587 VAL Chi-restraints excluded: chain DB residue 590 ASP Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 671 VAL Chi-restraints excluded: chain DB residue 693 SER Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 758 SER Chi-restraints excluded: chain DB residue 785 ASN Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 830 LEU Chi-restraints excluded: chain DB residue 831 ASN Chi-restraints excluded: chain DB residue 849 ASP Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 968 VAL Chi-restraints excluded: chain DB residue 969 THR Chi-restraints excluded: chain DB residue 1002 THR Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1020 ASP Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1142 VAL Chi-restraints excluded: chain DB residue 1165 SER Chi-restraints excluded: chain DB residue 1168 ASP Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 36 ASP Chi-restraints excluded: chain DC residue 46 ARG Chi-restraints excluded: chain DC residue 114 GLU Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 166 GLU Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 374 LEU Chi-restraints excluded: chain DC residue 379 LEU Chi-restraints excluded: chain DC residue 437 LEU Chi-restraints excluded: chain DC residue 464 THR Chi-restraints excluded: chain DC residue 467 THR Chi-restraints excluded: chain DC residue 475 LEU Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 506 SER Chi-restraints excluded: chain DC residue 513 SER Chi-restraints excluded: chain DC residue 525 THR Chi-restraints excluded: chain DC residue 540 LEU Chi-restraints excluded: chain DC residue 544 GLU Chi-restraints excluded: chain DC residue 569 LEU Chi-restraints excluded: chain DC residue 604 VAL Chi-restraints excluded: chain DC residue 632 LEU Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 749 GLU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 794 LEU Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 881 MET Chi-restraints excluded: chain DC residue 885 LEU Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 919 VAL Chi-restraints excluded: chain DC residue 953 MET Chi-restraints excluded: chain DC residue 960 VAL Chi-restraints excluded: chain DC residue 963 SER Chi-restraints excluded: chain DC residue 970 GLN Chi-restraints excluded: chain DC residue 985 VAL Chi-restraints excluded: chain DC residue 987 THR Chi-restraints excluded: chain DC residue 1025 THR Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1121 THR Chi-restraints excluded: chain DC residue 1128 ARG Chi-restraints excluded: chain DC residue 1133 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1161 LYS Chi-restraints excluded: chain DE residue 149 LEU Chi-restraints excluded: chain DE residue 154 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 246 ILE Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 319 ASN Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 405 ILE Chi-restraints excluded: chain DE residue 429 ILE Chi-restraints excluded: chain DE residue 466 VAL Chi-restraints excluded: chain DE residue 503 ASP Chi-restraints excluded: chain DE residue 529 ASP Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 586 THR Chi-restraints excluded: chain DE residue 591 LEU Chi-restraints excluded: chain DE residue 601 ILE Chi-restraints excluded: chain DE residue 651 ASN Chi-restraints excluded: chain DE residue 659 ARG Chi-restraints excluded: chain DE residue 678 THR Chi-restraints excluded: chain DE residue 698 GLN Chi-restraints excluded: chain DE residue 726 THR Chi-restraints excluded: chain DF residue 8 SER Chi-restraints excluded: chain DF residue 15 HIS Chi-restraints excluded: chain DF residue 19 THR Chi-restraints excluded: chain DF residue 22 LEU Chi-restraints excluded: chain DF residue 39 ARG Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 137 VAL Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 189 ASP Chi-restraints excluded: chain DF residue 192 LEU Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 246 LYS Chi-restraints excluded: chain DF residue 255 GLU Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 264 VAL Chi-restraints excluded: chain DF residue 297 ARG Chi-restraints excluded: chain DF residue 321 LEU Chi-restraints excluded: chain DF residue 332 GLU Chi-restraints excluded: chain DF residue 373 ASP Chi-restraints excluded: chain DF residue 395 LEU Chi-restraints excluded: chain DF residue 402 THR Chi-restraints excluded: chain DF residue 439 THR Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DF residue 568 LEU Chi-restraints excluded: chain DF residue 591 HIS Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 93 ARG Chi-restraints excluded: chain DG residue 95 VAL Chi-restraints excluded: chain DG residue 127 LEU Chi-restraints excluded: chain DG residue 130 LEU Chi-restraints excluded: chain DG residue 147 SER Chi-restraints excluded: chain DG residue 149 SER Chi-restraints excluded: chain DG residue 165 VAL Chi-restraints excluded: chain DG residue 176 VAL Chi-restraints excluded: chain DG residue 179 LEU Chi-restraints excluded: chain DG residue 186 ARG Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 296 ASP Chi-restraints excluded: chain DG residue 305 VAL Chi-restraints excluded: chain DG residue 318 ILE Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DG residue 473 CYS Chi-restraints excluded: chain DG residue 494 THR Chi-restraints excluded: chain DG residue 582 VAL Chi-restraints excluded: chain DG residue 615 SER Chi-restraints excluded: chain DG residue 616 ARG Chi-restraints excluded: chain DG residue 623 MET Chi-restraints excluded: chain DG residue 626 LEU Chi-restraints excluded: chain DH residue 1 MET Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 51 ARG Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 81 LYS Chi-restraints excluded: chain DH residue 83 GLU Chi-restraints excluded: chain DH residue 85 LEU Chi-restraints excluded: chain DH residue 174 LEU Chi-restraints excluded: chain DH residue 181 VAL Chi-restraints excluded: chain DH residue 195 TYR Chi-restraints excluded: chain DH residue 236 MET Chi-restraints excluded: chain DH residue 258 MET Chi-restraints excluded: chain DH residue 268 LEU Chi-restraints excluded: chain DH residue 273 SER Chi-restraints excluded: chain DH residue 297 CYS Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 323 SER Chi-restraints excluded: chain DH residue 344 VAL Chi-restraints excluded: chain DH residue 345 VAL Chi-restraints excluded: chain DH residue 350 VAL Chi-restraints excluded: chain DH residue 354 LEU Chi-restraints excluded: chain DH residue 364 ARG Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 382 PHE Chi-restraints excluded: chain DH residue 396 VAL Chi-restraints excluded: chain DH residue 411 LEU Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 486 THR Chi-restraints excluded: chain DH residue 495 THR Chi-restraints excluded: chain DH residue 557 VAL Chi-restraints excluded: chain DH residue 562 THR Chi-restraints excluded: chain DJ residue 16 ASN Chi-restraints excluded: chain DJ residue 46 ARG Chi-restraints excluded: chain DJ residue 54 SER Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 91 THR Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 110 LEU Chi-restraints excluded: chain DJ residue 137 MET Chi-restraints excluded: chain DJ residue 212 ASP Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 236 ARG Chi-restraints excluded: chain DJ residue 302 SER Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 2 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 172 LEU Chi-restraints excluded: chain DK residue 173 VAL Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DK residue 294 SER Chi-restraints excluded: chain DT residue 88 THR Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 131 SER Chi-restraints excluded: chain DT residue 137 LEU Chi-restraints excluded: chain DT residue 166 THR Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 26 THR Chi-restraints excluded: chain DV residue 39 ARG Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 71 GLN Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DV residue 178 THR Chi-restraints excluded: chain DV residue 180 ASP Chi-restraints excluded: chain DV residue 183 LEU Chi-restraints excluded: chain DW residue 12 THR Chi-restraints excluded: chain DW residue 58 ARG Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DX residue 34 LYS Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 136 ARG Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 23 SER Chi-restraints excluded: chain DY residue 43 LEU Chi-restraints excluded: chain DY residue 47 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 52 GLN Chi-restraints excluded: chain DY residue 64 ASP Chi-restraints excluded: chain DY residue 77 VAL Chi-restraints excluded: chain DY residue 81 THR Chi-restraints excluded: chain DY residue 93 THR Chi-restraints excluded: chain DY residue 113 VAL Chi-restraints excluded: chain CC residue 4 MET Chi-restraints excluded: chain CC residue 7 ILE Chi-restraints excluded: chain CC residue 14 THR Chi-restraints excluded: chain CC residue 21 PHE Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CC residue 72 ILE Chi-restraints excluded: chain CI residue 33 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 59 ARG Chi-restraints excluded: chain CI residue 65 MET Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 311 CYS Chi-restraints excluded: chain CI residue 324 ARG Chi-restraints excluded: chain CI residue 343 VAL Chi-restraints excluded: chain CI residue 356 MET Chi-restraints excluded: chain CI residue 372 ILE Chi-restraints excluded: chain CI residue 439 ARG Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 23 LYS Chi-restraints excluded: chain CJ residue 78 THR Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 141 ASP Chi-restraints excluded: chain CJ residue 162 ILE Chi-restraints excluded: chain CJ residue 202 ASP Chi-restraints excluded: chain CJ residue 257 VAL Chi-restraints excluded: chain CJ residue 273 ARG Chi-restraints excluded: chain CJ residue 287 LEU Chi-restraints excluded: chain CJ residue 325 SER Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 346 PRO Chi-restraints excluded: chain CJ residue 396 LYS Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 498 CYS Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 530 THR Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 565 THR Chi-restraints excluded: chain CJ residue 667 VAL Chi-restraints excluded: chain CJ residue 671 LEU Chi-restraints excluded: chain CJ residue 714 THR Chi-restraints excluded: chain CJ residue 724 THR Chi-restraints excluded: chain CJ residue 727 THR Chi-restraints excluded: chain CJ residue 731 MET Chi-restraints excluded: chain CJ residue 757 LEU Chi-restraints excluded: chain CJ residue 769 GLN Chi-restraints excluded: chain CJ residue 781 HIS Chi-restraints excluded: chain CJ residue 798 GLN Chi-restraints excluded: chain CK residue 15 ARG Chi-restraints excluded: chain CK residue 32 LEU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 47 ILE Chi-restraints excluded: chain CN residue 22 THR Chi-restraints excluded: chain CN residue 43 SER Chi-restraints excluded: chain CN residue 49 SER Chi-restraints excluded: chain CN residue 70 LYS Chi-restraints excluded: chain CN residue 72 THR Chi-restraints excluded: chain CN residue 77 ASN Chi-restraints excluded: chain CN residue 81 LEU Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CN residue 127 LEU Chi-restraints excluded: chain CN residue 135 THR Chi-restraints excluded: chain CN residue 158 ARG Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 45 ARG Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 107 THR Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain CS residue 121 SER Chi-restraints excluded: chain CS residue 140 MET Chi-restraints excluded: chain Cg residue 76 SER Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 120 LEU Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 143 THR Chi-restraints excluded: chain Cg residue 153 CYS Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 213 VAL Chi-restraints excluded: chain Cg residue 224 LEU Chi-restraints excluded: chain Cg residue 227 THR Chi-restraints excluded: chain Cg residue 233 THR Chi-restraints excluded: chain Cg residue 262 GLN Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 308 LEU Chi-restraints excluded: chain Cg residue 318 ILE Chi-restraints excluded: chain Cg residue 325 LEU Chi-restraints excluded: chain Cg residue 355 THR Chi-restraints excluded: chain Cg residue 357 THR Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 27 CYS Chi-restraints excluded: chain Ci residue 54 GLN Chi-restraints excluded: chain Ci residue 76 MET Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 105 ARG Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 164 ASN Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 57 ASP Chi-restraints excluded: chain Ck residue 86 GLU Chi-restraints excluded: chain Ck residue 87 ARG Chi-restraints excluded: chain Ck residue 93 THR Chi-restraints excluded: chain Ck residue 111 THR Chi-restraints excluded: chain Ck residue 136 ASP Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 214 LEU Chi-restraints excluded: chain Ck residue 290 LEU Chi-restraints excluded: chain Ck residue 317 VAL Chi-restraints excluded: chain Ck residue 320 VAL Chi-restraints excluded: chain Ck residue 337 VAL Chi-restraints excluded: chain Ck residue 353 ARG Chi-restraints excluded: chain Ck residue 370 THR Chi-restraints excluded: chain Ck residue 376 VAL Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 618 ILE Chi-restraints excluded: chain Ck residue 642 VAL Chi-restraints excluded: chain Ck residue 652 ARG Chi-restraints excluded: chain Ck residue 661 ILE Chi-restraints excluded: chain Ck residue 682 ASN Chi-restraints excluded: chain Ck residue 706 SER Chi-restraints excluded: chain Ck residue 733 LEU Chi-restraints excluded: chain Ck residue 760 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 770 optimal weight: 0.9980 chunk 691 optimal weight: 0.9990 chunk 383 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 466 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 714 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 434 optimal weight: 0.7980 chunk 532 optimal weight: 5.9990 chunk 828 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 221 HIS 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 785 ASN DB 908 GLN 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 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 DE 698 GLN ** 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 230 ASN ** 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 498 ASN DH 526 ASN ** DJ 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DJ 31 HIS DJ 33 ASN DJ 55 ASN DJ 82 GLN DJ 247 ASN DJ 260 ASN DJ 293 ASN DJ 301 HIS DJ 314 GLN DK 163 HIS DK 171 GLN 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 DW 23 HIS DW 66 HIS DW 71 GLN ** DW 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 99 HIS DW 121 HIS DW 154 HIS DW 167 GLN DX 58 HIS DX 113 HIS DY 10 ASN ** DY 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 781 HIS CJ 792 HIS CN 96 HIS CN 133 HIS CN 142 HIS CN 153 ASN CN 157 GLN ** CR 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 266 ASN CS 110 HIS CS 160 GLN Cg 164 HIS Cg 184 HIS Cg 251 HIS ** Cg 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 289 ASN Cg 301 HIS Ci 19 HIS Ci 29 GLN Ci 96 ASN Ci 112 ASN Ci 136 HIS 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 682 ASN Ck 728 GLN Total number of N/Q/H flips: 153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 79052 Z= 0.205 Angle : 0.607 9.016 107780 Z= 0.323 Chirality : 0.042 0.278 11595 Planarity : 0.005 0.097 13537 Dihedral : 14.008 171.440 13016 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 5.62 % Allowed : 14.89 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.01 % Twisted Proline : 0.19 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.08), residues: 8966 helix: 0.42 (0.08), residues: 4218 sheet: -0.35 (0.24), residues: 392 loop : -0.57 (0.09), residues: 4356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPCN 152 HIS 0.008 0.001 HISDB 737 PHE 0.024 0.002 PHECC 61 TYR 0.022 0.001 TYRDB 95 ARG 0.031 0.001 ARGDF 188 *********************** 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 1581 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 444 poor density : 1137 time to evaluate : 6.617 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: DA 1280 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8095 (mp0) REVERT: DA 1287 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8201 (mtm-85) REVERT: DL 42 PRO cc_start: 0.8294 (Cg_endo) cc_final: 0.8066 (Cg_exo) REVERT: DL 74 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.5035 (mmt180) REVERT: DL 80 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7333 (ptt180) REVERT: DL 100 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8827 (mt) REVERT: DL 269 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: DL 305 THR cc_start: 0.8923 (m) cc_final: 0.8634 (p) REVERT: DB 103 TYR cc_start: 0.8542 (m-80) cc_final: 0.8146 (m-10) REVERT: DB 265 GLU cc_start: 0.9271 (tt0) cc_final: 0.9006 (tt0) REVERT: DB 276 VAL cc_start: 0.8917 (p) cc_final: 0.8674 (m) REVERT: DB 311 MET cc_start: 0.9126 (tpt) cc_final: 0.8784 (tpt) REVERT: DB 369 GLN cc_start: 0.8897 (tt0) cc_final: 0.8604 (tt0) REVERT: DB 388 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (t) REVERT: DB 409 ASP cc_start: 0.9119 (m-30) cc_final: 0.8873 (m-30) REVERT: DB 416 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8647 (p0) REVERT: DB 436 GLU cc_start: 0.9334 (tm-30) cc_final: 0.8944 (tm-30) REVERT: DB 437 ASN cc_start: 0.8777 (m-40) cc_final: 0.8249 (m-40) REVERT: DB 582 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8406 (tt0) REVERT: DB 699 MET cc_start: 0.9022 (ttp) cc_final: 0.8724 (ttm) REVERT: DB 834 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8882 (mt) REVERT: DB 980 GLU cc_start: 0.9045 (pm20) cc_final: 0.8611 (tm-30) REVERT: DB 998 LYS cc_start: 0.8882 (ptmm) cc_final: 0.8652 (ptmm) REVERT: DB 1001 THR cc_start: 0.9150 (m) cc_final: 0.8915 (p) REVERT: DB 1167 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7965 (mtm110) REVERT: DB 1168 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7895 (t0) REVERT: DC 92 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8027 (t80) REVERT: DC 114 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: DC 168 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7287 (t80) REVERT: DC 411 LYS cc_start: 0.9254 (tttt) cc_final: 0.9030 (tttt) REVERT: DC 467 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8821 (p) REVERT: DC 498 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8029 (pp) REVERT: DC 534 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9000 (mt) REVERT: DC 882 ASP cc_start: 0.9155 (m-30) cc_final: 0.8879 (m-30) REVERT: DC 903 THR cc_start: 0.9094 (m) cc_final: 0.8805 (m) REVERT: DC 953 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7851 (tpp) REVERT: DC 987 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8949 (m) REVERT: DE 185 GLU cc_start: 0.8374 (tt0) cc_final: 0.8010 (tt0) REVERT: DE 209 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8706 (tt0) REVERT: DE 210 MET cc_start: 0.9009 (mmm) cc_final: 0.8674 (mmt) REVERT: DE 246 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8701 (tp) REVERT: DF 15 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.6999 (p-80) REVERT: DF 39 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8696 (ptt180) REVERT: DF 182 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8418 (mmm160) REVERT: DF 275 MET cc_start: 0.9190 (tpp) cc_final: 0.8911 (tpp) REVERT: DF 495 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9045 (mt-10) REVERT: DG 111 ARG cc_start: 0.8178 (mmt180) cc_final: 0.7795 (mtt180) REVERT: DG 151 SER cc_start: 0.8694 (m) cc_final: 0.8489 (p) REVERT: DG 175 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8691 (tp30) REVERT: DG 307 GLU cc_start: 0.9088 (pm20) cc_final: 0.8879 (tp30) REVERT: DG 318 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8670 (pt) REVERT: DG 342 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8301 (t0) REVERT: DG 471 GLU cc_start: 0.8591 (tp30) cc_final: 0.8382 (pm20) REVERT: DG 615 SER cc_start: 0.9060 (OUTLIER) cc_final: 0.8674 (p) REVERT: DG 626 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9126 (mt) REVERT: DH 71 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8387 (tp-100) REVERT: DH 364 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8642 (ttm170) REVERT: DH 382 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: DH 414 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9123 (mt) REVERT: DH 481 ILE cc_start: 0.9243 (pt) cc_final: 0.9041 (pt) REVERT: DJ 137 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9014 (tpt) REVERT: DJ 186 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8970 (ttmt) REVERT: DJ 187 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: DK 151 ASN cc_start: 0.9219 (m-40) cc_final: 0.8646 (m110) REVERT: DK 297 SER cc_start: 0.8496 (p) cc_final: 0.8248 (p) REVERT: DT 52 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8327 (ptm160) REVERT: DT 126 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8472 (ttp-110) REVERT: DT 205 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8771 (m) REVERT: DV 49 ASP cc_start: 0.9187 (t0) cc_final: 0.8892 (t70) REVERT: DW 87 ASN cc_start: 0.8991 (m-40) cc_final: 0.8436 (m-40) REVERT: DW 115 ASN cc_start: 0.8241 (m-40) cc_final: 0.7185 (t0) REVERT: DW 118 LYS cc_start: 0.8935 (mttt) cc_final: 0.8698 (mmmt) REVERT: DX 103 MET cc_start: 0.8645 (mtp) cc_final: 0.8421 (mtp) REVERT: DX 161 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.9060 (p) REVERT: CC 38 PHE cc_start: 0.9080 (m-10) cc_final: 0.8750 (m-80) REVERT: CC 60 SER cc_start: 0.8531 (p) cc_final: 0.8207 (p) REVERT: CI 1 MET cc_start: 0.7088 (tmm) cc_final: 0.6565 (ttt) REVERT: CI 38 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9082 (mt) REVERT: CI 290 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6828 (tt) REVERT: CJ 23 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8035 (mmtm) REVERT: CJ 345 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8666 (m) REVERT: CJ 370 MET cc_start: 0.9165 (ttp) cc_final: 0.8584 (ttp) REVERT: CJ 425 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7791 (ttp-110) REVERT: CJ 714 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8859 (p) REVERT: CJ 768 ASP cc_start: 0.9249 (t0) cc_final: 0.8874 (t0) REVERT: CJ 769 GLN cc_start: 0.8742 (tt0) cc_final: 0.8355 (mt0) REVERT: CK 20 MET cc_start: 0.8958 (mmp) cc_final: 0.8652 (tpt) REVERT: CK 52 ASP cc_start: 0.9364 (m-30) cc_final: 0.8706 (m-30) REVERT: CN 31 MET cc_start: 0.9258 (mtt) cc_final: 0.8961 (mtt) REVERT: CN 32 TYR cc_start: 0.9225 (m-80) cc_final: 0.8921 (m-80) REVERT: CN 38 ASP cc_start: 0.9269 (m-30) cc_final: 0.8906 (m-30) REVERT: CN 46 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8598 (mtp180) REVERT: CN 77 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8607 (m-40) REVERT: CN 86 TYR cc_start: 0.9167 (m-10) cc_final: 0.8814 (m-10) REVERT: CN 127 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9230 (tp) REVERT: CN 163 TYR cc_start: 0.9215 (m-80) cc_final: 0.9007 (m-80) REVERT: CR 277 SER cc_start: 0.8688 (p) cc_final: 0.8370 (p) REVERT: CS 75 MET cc_start: 0.9134 (mmm) cc_final: 0.8852 (mmm) REVERT: CS 140 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8783 (mmt) REVERT: CS 155 MET cc_start: 0.8918 (ttp) cc_final: 0.8714 (ttp) REVERT: Cg 32 MET cc_start: 0.9007 (tpt) cc_final: 0.8807 (tpt) REVERT: Cg 73 ASP cc_start: 0.9186 (m-30) cc_final: 0.8903 (m-30) REVERT: Cg 112 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8523 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8175 (p-80) REVERT: Ci 18 THR cc_start: 0.9437 (OUTLIER) cc_final: 0.8999 (p) REVERT: Ci 89 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8577 (tpp) REVERT: Ci 105 ARG cc_start: 0.9205 (ptt-90) cc_final: 0.9000 (tmm-80) REVERT: Ci 174 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7626 (t0) REVERT: Ck 60 MET cc_start: 0.7625 (ptm) cc_final: 0.6978 (mmm) REVERT: Ck 166 MET cc_start: 0.8162 (mmt) cc_final: 0.7742 (mmm) REVERT: Ck 272 ASP cc_start: 0.8835 (m-30) cc_final: 0.8253 (m-30) REVERT: Ck 292 ASP cc_start: 0.9022 (m-30) cc_final: 0.8353 (p0) REVERT: Ck 337 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8407 (t) REVERT: Ck 392 PHE cc_start: 0.8325 (t80) cc_final: 0.8105 (t80) REVERT: Ck 414 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7624 (ttm) REVERT: Ck 544 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8284 (ttp-110) REVERT: Ck 564 LEU cc_start: 0.8778 (mt) cc_final: 0.8443 (mt) REVERT: Ck 661 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.9018 (mt) REVERT: Ck 681 ASP cc_start: 0.9448 (t0) cc_final: 0.9020 (t0) REVERT: Ck 713 ASP cc_start: 0.9307 (m-30) cc_final: 0.9046 (m-30) outliers start: 444 outliers final: 226 residues processed: 1481 average time/residue: 0.8396 time to fit residues: 2085.1234 Evaluate side-chains 1219 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 945 time to evaluate : 6.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1240 LEU Chi-restraints excluded: chain DL residue 68 LEU Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 100 LEU Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 269 MET Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 286 THR Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 275 THR Chi-restraints excluded: chain DB residue 289 LEU Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 388 VAL Chi-restraints excluded: chain DB residue 416 ASN Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 473 VAL Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 553 LEU Chi-restraints excluded: chain DB residue 587 VAL Chi-restraints excluded: chain DB residue 590 ASP Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 785 ASN Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 834 ILE Chi-restraints excluded: chain DB residue 849 ASP Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 968 VAL Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1142 VAL Chi-restraints excluded: chain DB residue 1165 SER Chi-restraints excluded: chain DB residue 1168 ASP Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 114 GLU Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 168 PHE Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 406 GLN Chi-restraints excluded: chain DC residue 437 LEU Chi-restraints excluded: chain DC residue 464 THR Chi-restraints excluded: chain DC residue 467 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 513 SER Chi-restraints excluded: chain DC residue 525 THR Chi-restraints excluded: chain DC residue 534 LEU Chi-restraints excluded: chain DC residue 540 LEU Chi-restraints excluded: chain DC residue 594 GLU Chi-restraints excluded: chain DC residue 604 VAL Chi-restraints excluded: chain DC residue 632 LEU Chi-restraints excluded: chain DC residue 648 LEU Chi-restraints excluded: chain DC residue 676 GLN Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 953 MET Chi-restraints excluded: chain DC residue 960 VAL Chi-restraints excluded: chain DC residue 963 SER Chi-restraints excluded: chain DC residue 987 THR Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1121 THR Chi-restraints excluded: chain DC residue 1128 ARG Chi-restraints excluded: chain DC residue 1150 SER Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1159 ASP Chi-restraints excluded: chain DC residue 1161 LYS Chi-restraints excluded: chain DC residue 1162 SER Chi-restraints excluded: chain DE residue 65 ILE Chi-restraints excluded: chain DE residue 72 ARG Chi-restraints excluded: chain DE residue 149 LEU Chi-restraints excluded: chain DE residue 154 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 246 ILE Chi-restraints excluded: chain DE residue 319 ASN Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 512 LEU Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 586 THR Chi-restraints excluded: chain DE residue 678 THR Chi-restraints excluded: chain DE residue 697 THR Chi-restraints excluded: chain DE residue 718 SER Chi-restraints excluded: chain DF residue 8 SER Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 15 HIS Chi-restraints excluded: chain DF residue 39 ARG Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 226 THR Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 332 GLU Chi-restraints excluded: chain DF residue 395 LEU Chi-restraints excluded: chain DF residue 439 THR Chi-restraints excluded: chain DF residue 521 THR Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 176 VAL Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 220 THR Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 296 ASP Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 318 ILE Chi-restraints excluded: chain DG residue 342 ASN Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DG residue 577 LEU Chi-restraints excluded: chain DG residue 615 SER Chi-restraints excluded: chain DG residue 626 LEU Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 51 ARG Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 191 HIS Chi-restraints excluded: chain DH residue 268 LEU Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 345 VAL Chi-restraints excluded: chain DH residue 364 ARG Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 382 PHE Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DH residue 493 SER Chi-restraints excluded: chain DH residue 495 THR Chi-restraints excluded: chain DH residue 557 VAL Chi-restraints excluded: chain DH residue 562 THR Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 71 MET Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 110 LEU Chi-restraints excluded: chain DJ residue 137 MET Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 187 ASP Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 111 LEU Chi-restraints excluded: chain DK residue 172 LEU Chi-restraints excluded: chain DK residue 173 VAL Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 262 ASN Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DK residue 294 SER Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 131 SER Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 193 SER Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 26 THR Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DV residue 178 THR Chi-restraints excluded: chain DW residue 10 THR Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 74 SER Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 161 THR Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 64 ASP Chi-restraints excluded: chain DY residue 77 VAL Chi-restraints excluded: chain DY residue 93 THR Chi-restraints excluded: chain CC residue 21 PHE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 25 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 309 ARG Chi-restraints excluded: chain CI residue 343 VAL Chi-restraints excluded: chain CI residue 406 THR Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 23 LYS Chi-restraints excluded: chain CJ residue 78 THR Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 162 ILE Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 212 THR Chi-restraints excluded: chain CJ residue 287 LEU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 425 ARG Chi-restraints excluded: chain CJ residue 428 SER Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 565 THR Chi-restraints excluded: chain CJ residue 667 VAL Chi-restraints excluded: chain CJ residue 714 THR Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CK residue 32 LEU Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 22 THR Chi-restraints excluded: chain CN residue 72 THR Chi-restraints excluded: chain CN residue 77 ASN Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CN residue 127 LEU Chi-restraints excluded: chain CN residue 135 THR Chi-restraints excluded: chain CN residue 157 GLN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain CS residue 121 SER Chi-restraints excluded: chain CS residue 140 MET Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 143 THR Chi-restraints excluded: chain Cg residue 153 CYS Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 254 VAL Chi-restraints excluded: chain Cg residue 262 GLN Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 318 ILE Chi-restraints excluded: chain Cg residue 325 LEU Chi-restraints excluded: chain Cg residue 365 ASP Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 34 GLN Chi-restraints excluded: chain Ck residue 55 SER Chi-restraints excluded: chain Ck residue 57 ASP Chi-restraints excluded: chain Ck residue 136 ASP Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 176 THR Chi-restraints excluded: chain Ck residue 337 VAL Chi-restraints excluded: chain Ck residue 370 THR Chi-restraints excluded: chain Ck residue 383 ILE Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 414 MET Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 633 MET Chi-restraints excluded: chain Ck residue 661 ILE Chi-restraints excluded: chain Ck residue 806 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 460 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 689 optimal weight: 0.0060 chunk 563 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 829 optimal weight: 8.9990 chunk 896 optimal weight: 1.9990 chunk 738 optimal weight: 4.9990 chunk 822 optimal weight: 0.8980 chunk 282 optimal weight: 0.9990 chunk 665 optimal weight: 0.0770 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 239 GLN ** DB 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 414 GLN DB 539 GLN DB 729 GLN DB 958 ASN DB1004 GLN DC 128 HIS DC 676 GLN ** DC 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 916 HIS DC 920 HIS ** 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 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 272 HIS ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS DG 229 HIS DG 230 ASN DG 342 ASN DH 512 ASN DH 524 HIS DJ 36 GLN DV 51 ASN ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN ** DW 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 56 GLN CN 78 GLN CN 150 HIS CR 249 GLN CR 267 ASN Cg 262 GLN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cg 380 ASN Ck 32 GLN Ck 54 ASN Ck 589 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3186 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= 0.167 Angle : 0.523 9.086 107780 Z= 0.276 Chirality : 0.039 0.240 11595 Planarity : 0.004 0.090 13537 Dihedral : 12.626 176.249 12598 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 4.19 % Allowed : 16.39 % Favored : 79.42 % 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: 1.19 (0.08), residues: 4245 sheet: -0.10 (0.25), residues: 395 loop : -0.31 (0.10), residues: 4326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPCN 152 HIS 0.006 0.001 HISDB 541 PHE 0.021 0.001 PHEDC 123 TYR 0.016 0.001 TYRDB 95 ARG 0.013 0.000 ARGCk 397 *********************** 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 1353 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1022 time to evaluate : 6.545 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: DA 1209 ASP cc_start: 0.9227 (t0) cc_final: 0.8945 (t0) REVERT: DA 1254 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6754 (mtm180) REVERT: DA 1280 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8317 (mp0) REVERT: DL 74 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.5047 (mmt180) REVERT: DL 80 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7324 (ptt180) REVERT: DL 305 THR cc_start: 0.8829 (m) cc_final: 0.8574 (p) REVERT: DB 276 VAL cc_start: 0.8997 (p) cc_final: 0.8717 (m) REVERT: DB 388 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (t) REVERT: DB 409 ASP cc_start: 0.9116 (m-30) cc_final: 0.8836 (m-30) REVERT: DB 416 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8796 (p0) REVERT: DB 436 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8848 (tm-30) REVERT: DB 582 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8416 (tt0) REVERT: DB 980 GLU cc_start: 0.9074 (pm20) cc_final: 0.8629 (tm-30) REVERT: DB 1001 THR cc_start: 0.9090 (m) cc_final: 0.8877 (p) REVERT: DB 1167 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.8037 (mtm110) REVERT: DC 92 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7923 (t80) REVERT: DC 325 MET cc_start: 0.8341 (tpt) cc_final: 0.8133 (mmm) REVERT: DC 498 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8150 (pp) REVERT: DC 534 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9108 (mt) REVERT: DC 568 ASP cc_start: 0.8935 (t0) cc_final: 0.8683 (t0) REVERT: DC 868 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8010 (tt0) REVERT: DC 903 THR cc_start: 0.9101 (m) cc_final: 0.8850 (m) REVERT: DC 953 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: DE 49 MET cc_start: 0.9001 (mtp) cc_final: 0.8691 (mtm) REVERT: DE 147 MET cc_start: 0.8912 (mmm) cc_final: 0.8273 (mtt) REVERT: DE 185 GLU cc_start: 0.8429 (tt0) cc_final: 0.8142 (tt0) REVERT: DE 209 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8733 (tt0) REVERT: DE 246 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8778 (tp) REVERT: DF 15 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6738 (p-80) REVERT: DF 286 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.9136 (mmt-90) REVERT: DF 307 GLU cc_start: 0.9309 (pt0) cc_final: 0.9019 (pt0) REVERT: DF 495 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9087 (mt-10) REVERT: DG 111 ARG cc_start: 0.8322 (mmt180) cc_final: 0.7911 (mtt-85) REVERT: DG 239 ASP cc_start: 0.8876 (p0) cc_final: 0.8562 (p0) REVERT: DG 471 GLU cc_start: 0.8574 (tp30) cc_final: 0.8313 (pm20) REVERT: DH 141 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (tp) REVERT: DH 364 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8325 (mtp180) REVERT: DH 377 ASP cc_start: 0.9047 (t70) cc_final: 0.8601 (t0) REVERT: DH 382 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: DH 414 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9174 (mt) REVERT: DH 525 LEU cc_start: 0.9135 (tp) cc_final: 0.8772 (mt) REVERT: DH 544 LYS cc_start: 0.8782 (tppt) cc_final: 0.8494 (ttpt) REVERT: DJ 113 ASP cc_start: 0.8655 (t0) cc_final: 0.8410 (t0) REVERT: DJ 137 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.8971 (tpt) REVERT: DJ 186 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8891 (ttmt) REVERT: DK 151 ASN cc_start: 0.9160 (m-40) cc_final: 0.8607 (m-40) REVERT: DT 126 ARG cc_start: 0.8667 (ttp80) cc_final: 0.8451 (ttp-110) REVERT: DT 145 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: DT 205 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8878 (m) REVERT: DV 49 ASP cc_start: 0.9156 (t0) cc_final: 0.8922 (t0) REVERT: DV 56 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8465 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8685 (t0) cc_final: 0.8156 (t0) REVERT: DV 137 ARG cc_start: 0.8963 (mmt-90) cc_final: 0.8580 (mmt-90) REVERT: DW 87 ASN cc_start: 0.8706 (m-40) cc_final: 0.8341 (m-40) REVERT: DW 115 ASN cc_start: 0.8153 (m-40) cc_final: 0.7014 (t0) REVERT: DX 76 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.9021 (mmm160) REVERT: DX 103 MET cc_start: 0.8298 (mtp) cc_final: 0.7968 (mtp) REVERT: DX 134 LYS cc_start: 0.9168 (ttmt) cc_final: 0.8967 (tttm) REVERT: DX 161 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9089 (p) REVERT: CC 10 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8338 (t) REVERT: CC 60 SER cc_start: 0.8660 (p) cc_final: 0.8296 (p) REVERT: CI 1 MET cc_start: 0.6915 (tmm) cc_final: 0.6466 (ttt) REVERT: CI 38 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9033 (mt) REVERT: CI 290 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6616 (tt) REVERT: CI 345 ASP cc_start: 0.9326 (t0) cc_final: 0.9121 (t0) REVERT: CI 372 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9072 (mm) REVERT: CJ 23 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8043 (mmtm) REVERT: CJ 345 VAL cc_start: 0.8894 (OUTLIER) cc_final: 0.8548 (m) REVERT: CJ 370 MET cc_start: 0.9177 (ttp) cc_final: 0.8578 (ttp) REVERT: CJ 425 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7824 (ttp-110) REVERT: CJ 769 GLN cc_start: 0.8725 (tt0) cc_final: 0.8212 (mt0) REVERT: CK 20 MET cc_start: 0.8922 (mmp) cc_final: 0.8651 (tpt) REVERT: CK 52 ASP cc_start: 0.9271 (m-30) cc_final: 0.9040 (m-30) REVERT: CN 31 MET cc_start: 0.9281 (mtt) cc_final: 0.9045 (mtm) REVERT: CN 38 ASP cc_start: 0.9201 (m-30) cc_final: 0.8867 (m-30) REVERT: CN 72 THR cc_start: 0.9212 (t) cc_final: 0.8984 (p) REVERT: CN 163 TYR cc_start: 0.9190 (m-80) cc_final: 0.8956 (m-80) REVERT: CR 277 SER cc_start: 0.8666 (p) cc_final: 0.8372 (p) REVERT: CS 75 MET cc_start: 0.9176 (mmm) cc_final: 0.8773 (mmm) REVERT: CS 103 ARG cc_start: 0.9021 (mtp85) cc_final: 0.8791 (mtm110) REVERT: CS 140 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8692 (mmt) REVERT: CS 155 MET cc_start: 0.8889 (ttp) cc_final: 0.8606 (ttt) REVERT: Cg 127 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8161 (p-80) REVERT: Cg 238 ARG cc_start: 0.8885 (tpp-160) cc_final: 0.8683 (mmp-170) REVERT: Ci 18 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.8996 (p) REVERT: Ci 76 MET cc_start: 0.9260 (mmm) cc_final: 0.8976 (mmm) REVERT: Ci 89 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8465 (tpp) REVERT: Ci 105 ARG cc_start: 0.9189 (ptt-90) cc_final: 0.8980 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.8982 (OUTLIER) cc_final: 0.7890 (t70) REVERT: Ci 174 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7715 (t0) REVERT: Ck 38 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8595 (mm) REVERT: Ck 60 MET cc_start: 0.7529 (ptm) cc_final: 0.7064 (mtp) REVERT: Ck 166 MET cc_start: 0.8451 (mmt) cc_final: 0.8074 (mmm) REVERT: Ck 222 LEU cc_start: 0.8380 (mt) cc_final: 0.8094 (mt) REVERT: Ck 272 ASP cc_start: 0.8793 (m-30) cc_final: 0.8579 (m-30) REVERT: Ck 292 ASP cc_start: 0.9045 (m-30) cc_final: 0.8426 (t70) REVERT: Ck 337 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (t) REVERT: Ck 397 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.7692 (mtm-85) REVERT: Ck 414 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (ttm) REVERT: Ck 543 GLN cc_start: 0.8484 (tp40) cc_final: 0.7746 (tp40) REVERT: Ck 547 ASN cc_start: 0.8476 (m110) cc_final: 0.7746 (m110) REVERT: Ck 557 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7823 (ttm110) REVERT: Ck 564 LEU cc_start: 0.8788 (mt) cc_final: 0.8502 (mt) outliers start: 331 outliers final: 186 residues processed: 1278 average time/residue: 0.7885 time to fit residues: 1676.0168 Evaluate side-chains 1137 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 914 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1188 GLU Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1240 LEU Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 58 MET Chi-restraints excluded: chain DL residue 68 LEU Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 286 THR Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 388 VAL Chi-restraints excluded: chain DB residue 416 ASN Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 968 VAL Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1020 ASP Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1165 SER Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 169 ASP Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 435 LEU Chi-restraints excluded: chain DC residue 437 LEU Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 513 SER Chi-restraints excluded: chain DC residue 525 THR Chi-restraints excluded: chain DC residue 534 LEU Chi-restraints excluded: chain DC residue 594 GLU Chi-restraints excluded: chain DC residue 632 LEU Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 919 VAL Chi-restraints excluded: chain DC residue 925 ASP Chi-restraints excluded: chain DC residue 953 MET Chi-restraints excluded: chain DC residue 963 SER Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 72 ARG Chi-restraints excluded: chain DE residue 149 LEU Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 246 ILE Chi-restraints excluded: chain DE residue 547 THR Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 678 THR Chi-restraints excluded: chain DF residue 15 HIS Chi-restraints excluded: chain DF residue 58 ASP Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 286 ARG Chi-restraints excluded: chain DF residue 395 LEU Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 162 LEU Chi-restraints excluded: chain DG residue 166 GLU Chi-restraints excluded: chain DG residue 176 VAL Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 296 ASP Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 51 ARG Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 268 LEU Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 345 VAL Chi-restraints excluded: chain DH residue 364 ARG Chi-restraints excluded: chain DH residue 382 PHE Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DH residue 495 THR Chi-restraints excluded: chain DH residue 557 VAL Chi-restraints excluded: chain DJ residue 38 MET Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 137 MET Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 172 LEU Chi-restraints excluded: chain DK residue 173 VAL Chi-restraints excluded: chain DK residue 224 SER Chi-restraints excluded: chain DK residue 225 THR Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DK residue 294 SER Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 131 SER Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 145 GLU Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 26 THR Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DV residue 180 ASP Chi-restraints excluded: chain DW residue 10 THR Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DW residue 159 THR Chi-restraints excluded: chain DX residue 74 SER Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 161 THR Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 39 VAL Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 64 ASP Chi-restraints excluded: chain DY residue 77 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 56 LEU Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 372 ILE Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 420 ARG Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 23 LYS Chi-restraints excluded: chain CJ residue 42 ASN Chi-restraints excluded: chain CJ residue 43 GLU Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 162 ILE Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 212 THR Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 425 ARG Chi-restraints excluded: chain CJ residue 428 SER Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 565 THR Chi-restraints excluded: chain CJ residue 667 VAL Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 22 THR Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CN residue 135 THR Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain CS residue 140 MET Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 143 THR Chi-restraints excluded: chain Cg residue 145 PHE Chi-restraints excluded: chain Cg residue 233 THR Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 318 ILE Chi-restraints excluded: chain Cg residue 365 ASP Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 54 ASN Chi-restraints excluded: chain Ck residue 136 ASP Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 176 THR Chi-restraints excluded: chain Ck residue 337 VAL Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 414 MET Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 806 ASP Chi-restraints excluded: chain Ck residue 810 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 819 optimal weight: 1.9990 chunk 623 optimal weight: 0.9980 chunk 430 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 395 optimal weight: 6.9990 chunk 557 optimal weight: 5.9990 chunk 832 optimal weight: 6.9990 chunk 881 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 789 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 ** DB 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 152 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 414 GLN DB 908 GLN DB 958 ASN DB1004 GLN DB1061 GLN ** DC 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 67 ASN ** DE 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 578 GLN DF 198 HIS DF 396 GLN DF 512 ASN DF 520 GLN ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 569 GLN DG 143 HIS DG 182 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 58 HIS DH 160 ASN DJ 72 HIS DK 175 HIS ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN CC 34 ASN CI 12 HIS CI 55 GLN CJ 42 ASN ** CJ 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 621 ASN CJ 711 HIS ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 56 GLN CN 130 HIS CN 157 GLN CS 88 ASN CS 135 ASN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 543 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 79052 Z= 0.337 Angle : 0.585 9.852 107780 Z= 0.305 Chirality : 0.042 0.261 11595 Planarity : 0.005 0.096 13537 Dihedral : 12.260 176.021 12501 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 4.74 % Allowed : 16.34 % Favored : 78.93 % 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: 0.63 (0.09), residues: 8966 helix: 1.24 (0.08), residues: 4262 sheet: -0.11 (0.24), residues: 432 loop : -0.30 (0.10), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPDB 138 HIS 0.013 0.001 HISDH 272 PHE 0.023 0.002 PHEDC 123 TYR 0.023 0.002 TYRDB1088 ARG 0.013 0.001 ARGDB 577 *********************** 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 1313 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 939 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: DA 1280 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8355 (mp0) REVERT: DL 74 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.4759 (mmt180) REVERT: DL 80 ARG cc_start: 0.8061 (ttm110) cc_final: 0.7352 (ptt180) REVERT: DL 100 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8887 (mt) REVERT: DL 305 THR cc_start: 0.8982 (m) cc_final: 0.8694 (p) REVERT: DB 270 THR cc_start: 0.9374 (m) cc_final: 0.9165 (p) REVERT: DB 276 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8816 (m) REVERT: DB 409 ASP cc_start: 0.9158 (m-30) cc_final: 0.8936 (m-30) REVERT: DB 740 GLU cc_start: 0.8915 (tt0) cc_final: 0.8693 (tt0) REVERT: DB 1168 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.7978 (t0) REVERT: DC 62 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8924 (t) REVERT: DC 92 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.7821 (t80) REVERT: DC 344 MET cc_start: 0.7496 (mtp) cc_final: 0.6797 (tpp) REVERT: DC 498 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8325 (pp) REVERT: DC 868 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8350 (tt0) REVERT: DC 903 THR cc_start: 0.9249 (m) cc_final: 0.9045 (m) REVERT: DE 185 GLU cc_start: 0.8984 (tt0) cc_final: 0.8748 (tt0) REVERT: DE 246 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9077 (tp) REVERT: DF 15 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.6996 (p-80) REVERT: DF 182 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.6804 (mmm160) REVERT: DF 307 GLU cc_start: 0.9332 (pt0) cc_final: 0.9075 (pt0) REVERT: DF 439 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9330 (p) REVERT: DF 495 GLU cc_start: 0.9344 (mt-10) cc_final: 0.9123 (mt-10) REVERT: DG 111 ARG cc_start: 0.8230 (mmt180) cc_final: 0.7790 (mtt-85) REVERT: DG 294 MET cc_start: 0.9249 (ttp) cc_final: 0.9039 (mtp) REVERT: DG 471 GLU cc_start: 0.8697 (tp30) cc_final: 0.8420 (pm20) REVERT: DG 472 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7917 (ttm110) REVERT: DH 71 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8486 (tp-100) REVERT: DH 141 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9043 (tp) REVERT: DH 364 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8418 (mtp180) REVERT: DH 377 ASP cc_start: 0.9007 (t70) cc_final: 0.8695 (t0) REVERT: DH 414 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9153 (mt) REVERT: DH 544 LYS cc_start: 0.8819 (tppt) cc_final: 0.8595 (ttpt) REVERT: DJ 137 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9043 (tpt) REVERT: DJ 186 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8877 (ttmt) REVERT: DK 151 ASN cc_start: 0.9195 (m-40) cc_final: 0.8748 (m110) REVERT: DT 52 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8434 (ttm-80) REVERT: DT 126 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8636 (ttp-110) REVERT: DT 145 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: DV 49 ASP cc_start: 0.9306 (t0) cc_final: 0.9096 (t70) REVERT: DV 56 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8566 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8537 (t0) cc_final: 0.8044 (t0) REVERT: DW 115 ASN cc_start: 0.8154 (m-40) cc_final: 0.7068 (t0) REVERT: DX 52 GLU cc_start: 0.8874 (pt0) cc_final: 0.8475 (pt0) REVERT: DX 103 MET cc_start: 0.8708 (mtp) cc_final: 0.8287 (mtp) REVERT: DX 161 THR cc_start: 0.9367 (OUTLIER) cc_final: 0.9153 (p) REVERT: DY 65 LEU cc_start: 0.9164 (mp) cc_final: 0.8912 (mp) REVERT: CC 60 SER cc_start: 0.8702 (p) cc_final: 0.8329 (p) REVERT: CI 1 MET cc_start: 0.7046 (tmm) cc_final: 0.6515 (ttt) REVERT: CI 38 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9164 (mt) REVERT: CI 290 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6705 (tt) REVERT: CI 345 ASP cc_start: 0.9356 (t0) cc_final: 0.9059 (t0) REVERT: CJ 130 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8534 (ptt90) REVERT: CJ 152 GLN cc_start: 0.8246 (tt0) cc_final: 0.7262 (mm110) REVERT: CJ 345 VAL cc_start: 0.9303 (OUTLIER) cc_final: 0.8887 (m) REVERT: CJ 408 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8731 (tm-30) REVERT: CJ 769 GLN cc_start: 0.8708 (tt0) cc_final: 0.8339 (mt0) REVERT: CK 20 MET cc_start: 0.8854 (mmp) cc_final: 0.8621 (tpt) REVERT: CN 22 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9027 (p) REVERT: CN 38 ASP cc_start: 0.9307 (m-30) cc_final: 0.9057 (m-30) REVERT: CN 72 THR cc_start: 0.9126 (t) cc_final: 0.8860 (p) REVERT: CN 121 MET cc_start: 0.8815 (mtm) cc_final: 0.8594 (mtm) REVERT: CR 276 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7760 (mtt180) REVERT: CR 277 SER cc_start: 0.8868 (p) cc_final: 0.8614 (p) REVERT: CS 155 MET cc_start: 0.8854 (ttp) cc_final: 0.8464 (ttp) REVERT: Cg 127 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8153 (p-80) REVERT: Ci 82 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: Ci 89 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8513 (tpp) REVERT: Ci 105 ARG cc_start: 0.9167 (ptt-90) cc_final: 0.8859 (tmm-80) REVERT: Ci 174 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7791 (t0) REVERT: Ck 38 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9061 (mm) REVERT: Ck 60 MET cc_start: 0.7795 (ptm) cc_final: 0.7190 (mtp) REVERT: Ck 166 MET cc_start: 0.8625 (mmt) cc_final: 0.8314 (mmm) REVERT: Ck 222 LEU cc_start: 0.8469 (mt) cc_final: 0.8197 (mt) REVERT: Ck 272 ASP cc_start: 0.8882 (m-30) cc_final: 0.8646 (m-30) REVERT: Ck 337 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8258 (t) REVERT: Ck 397 ARG cc_start: 0.8305 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: Ck 564 LEU cc_start: 0.8723 (mt) cc_final: 0.8422 (mt) REVERT: Ck 568 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5909 (pp) outliers start: 374 outliers final: 236 residues processed: 1235 average time/residue: 0.7836 time to fit residues: 1608.6464 Evaluate side-chains 1136 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 868 time to evaluate : 6.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1191 ILE Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 58 MET Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 100 LEU Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 272 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 286 THR Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 276 VAL Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 503 ASN Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 522 MET Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 849 ASP Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 950 VAL Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1057 LEU Chi-restraints excluded: chain DB residue 1165 SER Chi-restraints excluded: chain DB residue 1168 ASP Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 62 SER Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 200 VAL Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 406 GLN Chi-restraints excluded: chain DC residue 437 LEU Chi-restraints excluded: chain DC residue 442 LEU Chi-restraints excluded: chain DC residue 474 LEU Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 632 LEU Chi-restraints excluded: chain DC residue 659 LEU Chi-restraints excluded: chain DC residue 695 VAL Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 919 VAL Chi-restraints excluded: chain DC residue 925 ASP Chi-restraints excluded: chain DC residue 963 SER Chi-restraints excluded: chain DC residue 1009 THR Chi-restraints excluded: chain DC residue 1066 LEU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1133 THR Chi-restraints excluded: chain DC residue 1150 SER Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1159 ASP Chi-restraints excluded: chain DC residue 1162 SER Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 65 ILE Chi-restraints excluded: chain DE residue 149 LEU Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 246 ILE Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 319 ASN Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 425 GLU Chi-restraints excluded: chain DE residue 512 LEU Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 678 THR Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 15 HIS Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 395 LEU Chi-restraints excluded: chain DF residue 402 THR Chi-restraints excluded: chain DF residue 439 THR Chi-restraints excluded: chain DF residue 454 SER Chi-restraints excluded: chain DF residue 512 ASN Chi-restraints excluded: chain DF residue 544 SER Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 34 ASP Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 84 LEU Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 97 VAL Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 323 VAL Chi-restraints excluded: chain DG residue 334 MET Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DG residue 450 MET Chi-restraints excluded: chain DG residue 472 ARG Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 51 ARG Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 174 LEU Chi-restraints excluded: chain DH residue 191 HIS Chi-restraints excluded: chain DH residue 249 MET Chi-restraints excluded: chain DH residue 268 LEU Chi-restraints excluded: chain DH residue 345 VAL Chi-restraints excluded: chain DH residue 364 ARG Chi-restraints excluded: chain DH residue 370 VAL Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 396 VAL Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DJ residue 15 VAL Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 137 MET Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 99 ASP Chi-restraints excluded: chain DK residue 111 LEU Chi-restraints excluded: chain DK residue 134 THR Chi-restraints excluded: chain DK residue 172 LEU Chi-restraints excluded: chain DK residue 173 VAL Chi-restraints excluded: chain DK residue 224 SER Chi-restraints excluded: chain DK residue 225 THR Chi-restraints excluded: chain DK residue 246 THR Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DK residue 294 SER Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 88 THR Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 145 GLU Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 26 THR Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 105 GLU Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 10 THR Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 83 THR Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 161 THR Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 39 VAL Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 77 VAL Chi-restraints excluded: chain DY residue 119 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 56 LEU Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 25 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 330 ASN Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 130 ARG Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 212 THR Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 379 ASP Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 565 THR Chi-restraints excluded: chain CJ residue 618 VAL Chi-restraints excluded: chain CJ residue 621 ASN Chi-restraints excluded: chain CJ residue 667 VAL Chi-restraints excluded: chain CJ residue 743 THR Chi-restraints excluded: chain CJ residue 757 LEU Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 798 GLN Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 22 THR Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CN residue 135 THR Chi-restraints excluded: chain CN residue 157 GLN Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 42 LEU Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 76 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 13 MET Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 100 THR Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 143 THR Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 254 VAL Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 316 THR Chi-restraints excluded: chain Cg residue 365 ASP Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 136 ASP Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 176 THR Chi-restraints excluded: chain Ck residue 254 ILE Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 337 VAL Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 633 MET Chi-restraints excluded: chain Ck residue 810 ILE 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: 1.9990 chunk 656 optimal weight: 0.7980 chunk 363 optimal weight: 4.9990 chunk 752 optimal weight: 2.9990 chunk 609 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 450 optimal weight: 0.8980 chunk 791 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 99 GLN ** 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 250 GLN DC 776 ASN DE 578 GLN ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 450 ASN DK 175 HIS DK 219 GLN DW 23 HIS ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN CI 55 GLN ** 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 ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 266 ASN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 34 GLN Ck 543 GLN Ck 547 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 79052 Z= 0.195 Angle : 0.507 8.524 107780 Z= 0.264 Chirality : 0.039 0.222 11595 Planarity : 0.004 0.097 13537 Dihedral : 11.958 177.126 12454 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Rotamer: Outliers : 3.62 % Allowed : 17.68 % Favored : 78.70 % 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: 0.86 (0.09), residues: 8966 helix: 1.46 (0.08), residues: 4256 sheet: 0.02 (0.25), residues: 407 loop : -0.22 (0.10), residues: 4303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPCk 693 HIS 0.018 0.001 HISDL 272 PHE 0.020 0.001 PHEDC 123 TYR 0.017 0.001 TYRDB 95 ARG 0.010 0.000 ARGDC 697 *********************** 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 1214 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 928 time to evaluate : 6.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1209 ASP cc_start: 0.9289 (t0) cc_final: 0.9029 (t0) REVERT: DA 1280 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8498 (mp0) REVERT: DL 74 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.4774 (mmt180) REVERT: DL 100 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9009 (mt) REVERT: DL 305 THR cc_start: 0.8916 (m) cc_final: 0.8585 (p) REVERT: DB 270 THR cc_start: 0.9356 (m) cc_final: 0.9143 (p) REVERT: DB 276 VAL cc_start: 0.9061 (p) cc_final: 0.8784 (m) REVERT: DB 370 GLN cc_start: 0.9015 (tt0) cc_final: 0.8694 (tm-30) REVERT: DB 374 GLU cc_start: 0.9166 (mp0) cc_final: 0.8961 (mp0) REVERT: DB 394 ASP cc_start: 0.8665 (m-30) cc_final: 0.8200 (p0) REVERT: DB 409 ASP cc_start: 0.9105 (m-30) cc_final: 0.8898 (m-30) REVERT: DB 1168 ASP cc_start: 0.8688 (m-30) cc_final: 0.7823 (t0) REVERT: DC 62 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.8964 (t) REVERT: DC 92 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7758 (t80) REVERT: DC 498 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8364 (pp) REVERT: DE 185 GLU cc_start: 0.8910 (tt0) cc_final: 0.8698 (tt0) REVERT: DE 246 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9074 (tp) REVERT: DF 92 MET cc_start: 0.9084 (ttm) cc_final: 0.8689 (ttp) REVERT: DF 159 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8370 (t0) REVERT: DF 495 GLU cc_start: 0.9309 (mt-10) cc_final: 0.9075 (mt-10) REVERT: DF 550 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9155 (m) REVERT: DG 111 ARG cc_start: 0.8179 (mmt180) cc_final: 0.7757 (mtt-85) REVERT: DG 471 GLU cc_start: 0.8730 (tp30) cc_final: 0.8480 (pm20) REVERT: DH 141 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9077 (tp) REVERT: DH 162 GLU cc_start: 0.9365 (tp30) cc_final: 0.9164 (tp30) REVERT: DH 377 ASP cc_start: 0.8973 (t70) cc_final: 0.8678 (t0) REVERT: DH 502 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8663 (mp0) REVERT: DH 543 MET cc_start: 0.8774 (tpp) cc_final: 0.8446 (mmp) REVERT: DH 544 LYS cc_start: 0.8820 (tppt) cc_final: 0.8597 (ttpt) REVERT: DJ 137 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9078 (tpt) REVERT: DJ 186 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8833 (ttmt) REVERT: DK 151 ASN cc_start: 0.9165 (m-40) cc_final: 0.8668 (m110) REVERT: DT 52 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8456 (ttm170) REVERT: DT 126 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8600 (ttp-110) REVERT: DT 145 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8332 (tm-30) REVERT: DV 49 ASP cc_start: 0.9258 (t0) cc_final: 0.9041 (t0) REVERT: DV 56 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8542 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8513 (t0) cc_final: 0.8211 (t0) REVERT: DW 115 ASN cc_start: 0.8141 (m-40) cc_final: 0.7124 (t0) REVERT: DX 52 GLU cc_start: 0.8846 (pt0) cc_final: 0.8484 (pt0) REVERT: DY 65 LEU cc_start: 0.9241 (mp) cc_final: 0.8905 (mp) REVERT: CC 10 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8687 (t) REVERT: CC 60 SER cc_start: 0.8745 (p) cc_final: 0.8395 (p) REVERT: CI 1 MET cc_start: 0.7057 (tmm) cc_final: 0.6578 (ttt) REVERT: CI 38 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9163 (mt) REVERT: CI 290 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6663 (tt) REVERT: CI 345 ASP cc_start: 0.9375 (t0) cc_final: 0.9072 (t0) REVERT: CJ 345 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8840 (m) REVERT: CJ 408 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8777 (tm-30) REVERT: CJ 769 GLN cc_start: 0.8733 (tt0) cc_final: 0.8383 (mt0) REVERT: CK 20 MET cc_start: 0.8794 (mmp) cc_final: 0.8590 (tpt) REVERT: CN 31 MET cc_start: 0.9292 (mtt) cc_final: 0.8823 (mtm) REVERT: CN 32 TYR cc_start: 0.9247 (m-80) cc_final: 0.8830 (m-80) REVERT: CN 72 THR cc_start: 0.9093 (t) cc_final: 0.8881 (p) REVERT: CR 276 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7787 (mtt180) REVERT: CR 277 SER cc_start: 0.8829 (p) cc_final: 0.8587 (p) REVERT: CS 139 GLU cc_start: 0.9002 (mp0) cc_final: 0.8794 (mp0) REVERT: CS 155 MET cc_start: 0.8815 (ttp) cc_final: 0.8459 (ttp) REVERT: CS 166 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8023 (ttm110) REVERT: Cg 127 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8043 (p-80) REVERT: Ci 82 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: Ci 89 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: Ci 105 ARG cc_start: 0.9163 (ptt-90) cc_final: 0.8933 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8011 (t70) REVERT: Ci 174 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7821 (t0) REVERT: Ck 38 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9037 (mm) REVERT: Ck 60 MET cc_start: 0.7750 (ptm) cc_final: 0.7268 (mtp) REVERT: Ck 166 MET cc_start: 0.8637 (mmt) cc_final: 0.8356 (mmm) REVERT: Ck 222 LEU cc_start: 0.8408 (mt) cc_final: 0.8142 (mt) REVERT: Ck 272 ASP cc_start: 0.8814 (m-30) cc_final: 0.8588 (m-30) REVERT: Ck 397 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7972 (mtm-85) REVERT: Ck 564 LEU cc_start: 0.8794 (mt) cc_final: 0.8475 (mt) REVERT: Ck 568 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5755 (pp) REVERT: Ck 843 MET cc_start: 0.5415 (ttt) cc_final: 0.5189 (ttp) outliers start: 286 outliers final: 202 residues processed: 1155 average time/residue: 0.7867 time to fit residues: 1507.8631 Evaluate side-chains 1111 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 884 time to evaluate : 7.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1188 GLU Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1244 LYS Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 58 MET Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 100 LEU Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 124 GLN Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 809 MET Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1165 SER Chi-restraints excluded: chain DB residue 1180 GLN Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 62 SER Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 200 VAL Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 406 GLN Chi-restraints excluded: chain DC residue 437 LEU Chi-restraints excluded: chain DC residue 442 LEU Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 533 LEU Chi-restraints excluded: chain DC residue 594 GLU Chi-restraints excluded: chain DC residue 632 LEU Chi-restraints excluded: chain DC residue 659 LEU Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 963 SER Chi-restraints excluded: chain DC residue 1014 SER Chi-restraints excluded: chain DC residue 1066 LEU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1159 ASP Chi-restraints excluded: chain DC residue 1162 SER Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 246 ILE Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 678 THR Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 15 HIS Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 395 LEU Chi-restraints excluded: chain DF residue 513 SER Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 162 LEU Chi-restraints excluded: chain DG residue 166 GLU Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 334 MET Chi-restraints excluded: chain DG residue 362 SER Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 51 ARG Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 191 HIS Chi-restraints excluded: chain DH residue 345 VAL Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 396 VAL Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DH residue 502 GLU Chi-restraints excluded: chain DH residue 553 LEU Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 137 MET Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 99 ASP Chi-restraints excluded: chain DK residue 172 LEU Chi-restraints excluded: chain DK residue 173 VAL Chi-restraints excluded: chain DK residue 224 SER Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 88 THR Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 145 GLU Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 26 THR Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 105 GLU Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 10 THR Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 77 VAL Chi-restraints excluded: chain DY residue 91 LEU Chi-restraints excluded: chain DY residue 119 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 56 LEU Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 25 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 212 THR Chi-restraints excluded: chain CJ residue 235 GLU Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 526 THR Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 625 VAL Chi-restraints excluded: chain CJ residue 757 LEU Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CK residue 35 GLN Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 22 THR Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 76 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 254 VAL Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 136 ASP Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 337 VAL Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE 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: 1.9990 chunk 174 optimal weight: 4.9990 chunk 517 optimal weight: 4.9990 chunk 217 optimal weight: 0.0010 chunk 882 optimal weight: 2.9990 chunk 732 optimal weight: 1.9990 chunk 408 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 463 optimal weight: 5.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- 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 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 414 GLN ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DE 650 HIS ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DH 123 HIS ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 25 HIS CC 67 ASN CJ 42 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 575 HIS ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 267 ASN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 79 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 79052 Z= 0.204 Angle : 0.497 9.650 107780 Z= 0.258 Chirality : 0.039 0.209 11595 Planarity : 0.004 0.088 13537 Dihedral : 11.755 177.009 12437 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 3.65 % Allowed : 17.66 % Favored : 78.69 % 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: 0.99 (0.09), residues: 8966 helix: 1.57 (0.08), residues: 4253 sheet: 0.16 (0.25), residues: 401 loop : -0.15 (0.10), residues: 4312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPCN 152 HIS 0.007 0.001 HISDW 23 PHE 0.018 0.001 PHEDC 123 TYR 0.016 0.001 TYRDB 95 ARG 0.010 0.000 ARGDA1197 *********************** 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 1213 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 925 time to evaluate : 6.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1280 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8463 (mp0) REVERT: DA 1295 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: DL 74 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.4753 (mmt180) REVERT: DL 80 ARG cc_start: 0.8077 (mtp-110) cc_final: 0.7779 (mmm160) REVERT: DL 286 THR cc_start: 0.9026 (p) cc_final: 0.8781 (p) REVERT: DL 305 THR cc_start: 0.8885 (m) cc_final: 0.8580 (p) REVERT: DB 270 THR cc_start: 0.9369 (m) cc_final: 0.9150 (p) REVERT: DB 276 VAL cc_start: 0.9065 (p) cc_final: 0.8786 (m) REVERT: DB 394 ASP cc_start: 0.8474 (m-30) cc_final: 0.8177 (p0) REVERT: DB 409 ASP cc_start: 0.9126 (m-30) cc_final: 0.8912 (m-30) REVERT: DB 976 THR cc_start: 0.8653 (p) cc_final: 0.8387 (p) REVERT: DB 978 ASN cc_start: 0.7263 (OUTLIER) cc_final: 0.6868 (p0) REVERT: DB 1168 ASP cc_start: 0.8728 (m-30) cc_final: 0.7943 (t0) REVERT: DC 62 SER cc_start: 0.9237 (OUTLIER) cc_final: 0.8901 (t) REVERT: DC 92 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7763 (t80) REVERT: DC 200 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8916 (m) REVERT: DC 344 MET cc_start: 0.7618 (mtp) cc_final: 0.6787 (tpp) REVERT: DC 498 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8398 (pp) REVERT: DE 49 MET cc_start: 0.8852 (mtp) cc_final: 0.8550 (mtm) REVERT: DE 185 GLU cc_start: 0.8949 (tt0) cc_final: 0.8732 (tt0) REVERT: DF 159 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8313 (t0) REVERT: DF 495 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9000 (mt-10) REVERT: DF 550 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9140 (m) REVERT: DG 111 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7725 (mtt-85) REVERT: DG 226 GLU cc_start: 0.8982 (tp30) cc_final: 0.8689 (tp30) REVERT: DG 294 MET cc_start: 0.8985 (mtp) cc_final: 0.8743 (mtm) REVERT: DG 471 GLU cc_start: 0.8724 (tp30) cc_final: 0.8485 (pm20) REVERT: DH 141 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9081 (tp) REVERT: DH 377 ASP cc_start: 0.8978 (t70) cc_final: 0.8710 (t0) REVERT: DH 414 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9120 (mt) REVERT: DH 452 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8212 (ttp-110) REVERT: DH 484 ASP cc_start: 0.9056 (m-30) cc_final: 0.8846 (m-30) REVERT: DH 543 MET cc_start: 0.8716 (tpp) cc_final: 0.8367 (mmp) REVERT: DH 544 LYS cc_start: 0.8850 (tppt) cc_final: 0.8628 (ttpt) REVERT: DJ 186 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8773 (ttmt) REVERT: DK 151 ASN cc_start: 0.9115 (m-40) cc_final: 0.8777 (m110) REVERT: DT 52 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8449 (ttm170) REVERT: DT 126 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8498 (ttp-110) REVERT: DT 145 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: DV 49 ASP cc_start: 0.9318 (t0) cc_final: 0.9117 (t70) REVERT: DV 56 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8466 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8541 (t0) cc_final: 0.8226 (t0) REVERT: DX 52 GLU cc_start: 0.8874 (pt0) cc_final: 0.8522 (pt0) REVERT: DX 103 MET cc_start: 0.8440 (mtp) cc_final: 0.8200 (mtp) REVERT: CC 10 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8694 (t) REVERT: CC 60 SER cc_start: 0.8718 (p) cc_final: 0.8391 (p) REVERT: CI 1 MET cc_start: 0.7111 (tmm) cc_final: 0.6702 (ttt) REVERT: CI 38 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9142 (mt) REVERT: CI 290 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6537 (tt) REVERT: CI 345 ASP cc_start: 0.9357 (t0) cc_final: 0.9142 (t0) REVERT: CJ 50 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8808 (m-30) REVERT: CJ 152 GLN cc_start: 0.8243 (tt0) cc_final: 0.7321 (mm110) REVERT: CJ 345 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8794 (m) REVERT: CJ 769 GLN cc_start: 0.8832 (tt0) cc_final: 0.8462 (mt0) REVERT: CN 31 MET cc_start: 0.9315 (mtt) cc_final: 0.8889 (mtm) REVERT: CN 32 TYR cc_start: 0.9240 (m-80) cc_final: 0.8832 (m-80) REVERT: CN 46 ARG cc_start: 0.8800 (mmm160) cc_final: 0.8529 (mtp180) REVERT: CN 72 THR cc_start: 0.9161 (t) cc_final: 0.8956 (p) REVERT: CR 276 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7977 (mtt180) REVERT: CR 277 SER cc_start: 0.8843 (p) cc_final: 0.8618 (p) REVERT: CS 152 ASP cc_start: 0.8515 (p0) cc_final: 0.7978 (p0) REVERT: CS 155 MET cc_start: 0.8795 (ttp) cc_final: 0.8392 (ttp) REVERT: Cg 112 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8102 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8007 (p-80) REVERT: Cg 238 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8462 (mmp-170) REVERT: Ci 82 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: Ci 89 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8451 (tpp) REVERT: Ci 105 ARG cc_start: 0.9154 (ptt-90) cc_final: 0.8945 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8075 (t70) REVERT: Ci 174 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7897 (t0) REVERT: Ck 38 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9065 (mm) REVERT: Ck 60 MET cc_start: 0.7748 (ptm) cc_final: 0.7294 (mtp) REVERT: Ck 166 MET cc_start: 0.8601 (mmt) cc_final: 0.8333 (mmm) REVERT: Ck 222 LEU cc_start: 0.8404 (mt) cc_final: 0.8158 (mt) REVERT: Ck 272 ASP cc_start: 0.8788 (m-30) cc_final: 0.8561 (m-30) REVERT: Ck 364 LEU cc_start: 0.7962 (mt) cc_final: 0.7669 (mp) REVERT: Ck 397 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: Ck 404 THR cc_start: 0.8767 (m) cc_final: 0.8460 (t) REVERT: Ck 544 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.7811 (ttp-110) REVERT: Ck 547 ASN cc_start: 0.8762 (m-40) cc_final: 0.8416 (m110) REVERT: Ck 564 LEU cc_start: 0.8716 (mt) cc_final: 0.8410 (mt) REVERT: Ck 568 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6087 (pp) REVERT: Ck 843 MET cc_start: 0.5417 (ttt) cc_final: 0.5185 (ttp) outliers start: 288 outliers final: 202 residues processed: 1153 average time/residue: 0.7731 time to fit residues: 1482.9976 Evaluate side-chains 1109 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 879 time to evaluate : 6.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1244 LYS Chi-restraints excluded: chain DA residue 1295 GLN Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 58 MET Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 522 MET Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 809 MET Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 949 THR Chi-restraints excluded: chain DB residue 978 ASN Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1057 LEU Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 62 SER Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 200 VAL Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 406 GLN Chi-restraints excluded: chain DC residue 435 LEU Chi-restraints excluded: chain DC residue 442 LEU Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 525 THR Chi-restraints excluded: chain DC residue 533 LEU Chi-restraints excluded: chain DC residue 659 LEU Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 952 GLU Chi-restraints excluded: chain DC residue 1066 LEU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1162 SER Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 327 ASN Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 80 VAL Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 544 SER Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 162 LEU Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 334 MET Chi-restraints excluded: chain DG residue 362 SER Chi-restraints excluded: chain DG residue 379 VAL Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DG residue 450 MET Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 144 ASP Chi-restraints excluded: chain DH residue 191 HIS Chi-restraints excluded: chain DH residue 249 MET Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 396 VAL Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 452 ARG Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DH residue 553 LEU Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 134 THR Chi-restraints excluded: chain DK residue 224 SER Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 88 THR Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 103 LEU Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 145 GLU Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 10 THR Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 74 SER Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 92 LYS Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 39 VAL Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 119 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 49 ILE Chi-restraints excluded: chain CC residue 56 LEU Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 25 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 313 ASP Chi-restraints excluded: chain CI residue 330 ASN Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 420 ARG Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 50 ASP Chi-restraints excluded: chain CJ residue 84 MET Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 212 THR Chi-restraints excluded: chain CJ residue 235 GLU Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 623 THR Chi-restraints excluded: chain CJ residue 757 LEU Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 777 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 42 LEU Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 76 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 254 VAL Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 316 THR Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 84 THR Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE 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: 0.4980 chunk 502 optimal weight: 1.9990 chunk 644 optimal weight: 3.9990 chunk 499 optimal weight: 0.6980 chunk 742 optimal weight: 4.9990 chunk 492 optimal weight: 0.7980 chunk 879 optimal weight: 4.9990 chunk 550 optimal weight: 4.9990 chunk 535 optimal weight: 0.8980 chunk 405 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DL 272 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 414 GLN DB 426 HIS DB 503 ASN ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 970 GLN ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DF 446 HIS ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS DG 249 GLN ** DG 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DK 219 GLN DT 9 GLN DW 23 HIS ** DW 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 72 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DX 167 HIS ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 267 ASN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 34 GLN Ck 385 HIS Ck 723 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 79052 Z= 0.185 Angle : 0.488 9.448 107780 Z= 0.252 Chirality : 0.038 0.243 11595 Planarity : 0.004 0.088 13537 Dihedral : 11.592 177.253 12407 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 3.39 % Allowed : 18.22 % Favored : 78.38 % 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: 1.10 (0.09), residues: 8966 helix: 1.65 (0.08), residues: 4254 sheet: 0.20 (0.26), residues: 401 loop : -0.08 (0.10), residues: 4311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPCk 693 HIS 0.006 0.001 HISDB 541 PHE 0.018 0.001 PHEDC 123 TYR 0.015 0.001 TYRDB 95 ARG 0.009 0.000 ARGDE 166 *********************** 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 1179 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 911 time to evaluate : 6.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1280 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8599 (mp0) REVERT: DA 1295 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: DA 1296 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8633 (mm-30) REVERT: DL 74 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.4722 (mmt180) REVERT: DL 80 ARG cc_start: 0.8073 (mtp-110) cc_final: 0.7678 (mtm180) REVERT: DL 100 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8896 (mt) REVERT: DL 282 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.8317 (t60) REVERT: DL 305 THR cc_start: 0.8871 (m) cc_final: 0.8565 (p) REVERT: DB 270 THR cc_start: 0.9362 (m) cc_final: 0.9153 (p) REVERT: DB 276 VAL cc_start: 0.9038 (p) cc_final: 0.8742 (m) REVERT: DB 370 GLN cc_start: 0.8990 (tt0) cc_final: 0.8756 (tm-30) REVERT: DB 394 ASP cc_start: 0.8575 (m-30) cc_final: 0.8258 (p0) REVERT: DB 409 ASP cc_start: 0.9112 (m-30) cc_final: 0.8894 (m-30) REVERT: DB 874 GLU cc_start: 0.9435 (tp30) cc_final: 0.9234 (tp30) REVERT: DB 1168 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.7917 (t0) REVERT: DC 62 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8869 (t) REVERT: DC 92 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7770 (t80) REVERT: DC 498 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8401 (pp) REVERT: DC 533 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9047 (mp) REVERT: DE 601 ILE cc_start: 0.9402 (mt) cc_final: 0.9196 (mt) REVERT: DE 634 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8889 (mtt90) REVERT: DF 159 ASP cc_start: 0.8898 (t0) cc_final: 0.8228 (t0) REVERT: DF 544 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.9021 (t) REVERT: DF 550 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9142 (m) REVERT: DG 15 ARG cc_start: 0.9024 (mtt-85) cc_final: 0.8806 (mtt-85) REVERT: DG 111 ARG cc_start: 0.8010 (mmt180) cc_final: 0.7706 (mtt-85) REVERT: DG 226 GLU cc_start: 0.8999 (tp30) cc_final: 0.8684 (tp30) REVERT: DG 294 MET cc_start: 0.8978 (mtp) cc_final: 0.8744 (mtm) REVERT: DG 471 GLU cc_start: 0.8736 (tp30) cc_final: 0.8511 (pm20) REVERT: DH 141 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9073 (tp) REVERT: DH 377 ASP cc_start: 0.8957 (t70) cc_final: 0.8704 (t0) REVERT: DH 414 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9111 (mt) REVERT: DH 484 ASP cc_start: 0.9057 (m-30) cc_final: 0.8843 (m-30) REVERT: DH 543 MET cc_start: 0.8674 (tpp) cc_final: 0.8334 (mmp) REVERT: DH 544 LYS cc_start: 0.8851 (tppt) cc_final: 0.8544 (tmtt) REVERT: DK 135 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8602 (tpp-160) REVERT: DK 151 ASN cc_start: 0.9106 (m-40) cc_final: 0.8761 (m110) REVERT: DT 52 ARG cc_start: 0.9004 (ttp80) cc_final: 0.8446 (ttm170) REVERT: DT 126 ARG cc_start: 0.8871 (ttp80) cc_final: 0.8522 (ttp-110) REVERT: DV 49 ASP cc_start: 0.9324 (t0) cc_final: 0.9114 (t0) REVERT: DV 56 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8504 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8533 (t0) cc_final: 0.8258 (t0) REVERT: DX 52 GLU cc_start: 0.8897 (pt0) cc_final: 0.8553 (pt0) REVERT: DX 103 MET cc_start: 0.8492 (mtp) cc_final: 0.8270 (mtp) REVERT: CC 10 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8703 (t) REVERT: CC 60 SER cc_start: 0.8686 (p) cc_final: 0.8384 (p) REVERT: CI 1 MET cc_start: 0.7140 (tmm) cc_final: 0.6656 (ttt) REVERT: CI 38 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9143 (mt) REVERT: CI 290 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6433 (tt) REVERT: CJ 37 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.5971 (t0) REVERT: CJ 130 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8575 (ptt90) REVERT: CJ 152 GLN cc_start: 0.8302 (tt0) cc_final: 0.7509 (mm110) REVERT: CJ 345 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8773 (m) REVERT: CJ 747 GLU cc_start: 0.8756 (pt0) cc_final: 0.8452 (tt0) REVERT: CJ 769 GLN cc_start: 0.8861 (tt0) cc_final: 0.8485 (mt0) REVERT: CK 52 ASP cc_start: 0.9192 (m-30) cc_final: 0.8800 (m-30) REVERT: CN 31 MET cc_start: 0.9323 (mtt) cc_final: 0.8917 (mtm) REVERT: CN 32 TYR cc_start: 0.9225 (m-80) cc_final: 0.8819 (m-80) REVERT: CN 46 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8504 (mtp180) REVERT: CR 276 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7915 (mtt180) REVERT: CR 277 SER cc_start: 0.8842 (p) cc_final: 0.8627 (p) REVERT: CS 152 ASP cc_start: 0.8525 (p0) cc_final: 0.8026 (p0) REVERT: Cg 112 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8099 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8005 (p-80) REVERT: Cg 238 ARG cc_start: 0.8697 (tpp-160) cc_final: 0.8433 (mmp-170) REVERT: Ci 82 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: Ci 89 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8447 (tpp) REVERT: Ci 105 ARG cc_start: 0.9219 (ptt-90) cc_final: 0.8966 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8056 (t70) REVERT: Ci 174 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7963 (t0) REVERT: Ck 38 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9063 (mm) REVERT: Ck 60 MET cc_start: 0.7609 (ptm) cc_final: 0.7214 (mtp) REVERT: Ck 166 MET cc_start: 0.8641 (mmt) cc_final: 0.8384 (mmm) REVERT: Ck 222 LEU cc_start: 0.8397 (mt) cc_final: 0.8163 (mt) REVERT: Ck 272 ASP cc_start: 0.8774 (m-30) cc_final: 0.8545 (m-30) REVERT: Ck 364 LEU cc_start: 0.7931 (mt) cc_final: 0.7617 (mp) REVERT: Ck 397 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7941 (mtm-85) REVERT: Ck 404 THR cc_start: 0.8716 (m) cc_final: 0.8395 (t) REVERT: Ck 547 ASN cc_start: 0.8769 (m-40) cc_final: 0.8424 (m110) REVERT: Ck 564 LEU cc_start: 0.8639 (mt) cc_final: 0.8345 (mt) REVERT: Ck 568 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6161 (pp) REVERT: Ck 843 MET cc_start: 0.5420 (ttt) cc_final: 0.5180 (ttp) outliers start: 268 outliers final: 191 residues processed: 1126 average time/residue: 0.7839 time to fit residues: 1467.9072 Evaluate side-chains 1100 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 880 time to evaluate : 6.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1295 GLN Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 100 LEU Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 272 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 282 TRP Chi-restraints excluded: chain DB residue 118 VAL Chi-restraints excluded: chain DB residue 137 VAL Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 522 MET Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 637 THR Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 809 MET Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 949 THR Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DB residue 1013 ARG Chi-restraints excluded: chain DB residue 1104 ASP Chi-restraints excluded: chain DB residue 1168 ASP Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 62 SER Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 353 LEU Chi-restraints excluded: chain DC residue 406 GLN Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 525 THR Chi-restraints excluded: chain DC residue 533 LEU Chi-restraints excluded: chain DC residue 569 LEU Chi-restraints excluded: chain DC residue 594 GLU Chi-restraints excluded: chain DC residue 659 LEU Chi-restraints excluded: chain DC residue 705 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 952 GLU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1121 THR Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DC residue 1159 ASP Chi-restraints excluded: chain DC residue 1162 SER Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 572 VAL Chi-restraints excluded: chain DE residue 634 ARG Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 58 ASP Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 194 THR Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 226 THR Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 544 SER Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 100 ASP Chi-restraints excluded: chain DG residue 162 LEU Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 323 VAL Chi-restraints excluded: chain DG residue 367 SER Chi-restraints excluded: chain DG residue 379 VAL Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 144 ASP Chi-restraints excluded: chain DH residue 191 HIS Chi-restraints excluded: chain DH residue 249 MET Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 375 VAL Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DH residue 553 LEU Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 58 VAL Chi-restraints excluded: chain DK residue 134 THR Chi-restraints excluded: chain DK residue 250 VAL Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 103 LEU Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DT residue 241 ASN Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 70 LEU Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 92 LYS Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 91 LEU Chi-restraints excluded: chain DY residue 119 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 29 SER Chi-restraints excluded: chain CC residue 49 ILE Chi-restraints excluded: chain CC residue 56 LEU Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 25 SER Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 290 ILE Chi-restraints excluded: chain CI residue 313 ASP Chi-restraints excluded: chain CI residue 351 MET Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 37 ASN Chi-restraints excluded: chain CJ residue 65 VAL Chi-restraints excluded: chain CJ residue 130 ARG Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 235 GLU Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 480 THR Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 517 VAL Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 757 LEU Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 777 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 269 SER Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 76 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 254 VAL Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 18 THR Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 34 GLN Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 543 optimal weight: 4.9990 chunk 351 optimal weight: 0.0000 chunk 524 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 172 optimal weight: 0.0170 chunk 170 optimal weight: 1.9990 chunk 558 optimal weight: 0.3980 chunk 598 optimal weight: 2.9990 chunk 434 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 690 optimal weight: 0.5980 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1243 GLN ** 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 503 ASN ** DB 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DG 143 HIS DG 351 GLN ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 9 GLN DT 240 GLN DV 175 GLN DW 23 HIS DW 72 GLN DW 119 GLN ** DW 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DY 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 55 GLN ** 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 762 GLN ** CJ 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 267 ASN ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 79052 Z= 0.133 Angle : 0.468 10.051 107780 Z= 0.242 Chirality : 0.037 0.290 11595 Planarity : 0.004 0.087 13537 Dihedral : 11.395 178.218 12396 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 2.52 % Allowed : 19.12 % Favored : 78.36 % 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: 1.25 (0.09), residues: 8966 helix: 1.77 (0.08), residues: 4239 sheet: 0.31 (0.26), residues: 403 loop : 0.00 (0.10), residues: 4324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPCk 693 HIS 0.020 0.001 HISDL 272 PHE 0.018 0.001 PHECJ 382 TYR 0.015 0.001 TYRDE 532 ARG 0.010 0.000 ARGDB 963 *********************** 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 1135 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 936 time to evaluate : 6.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1254 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6966 (mtm180) REVERT: DA 1280 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8564 (mp0) REVERT: DA 1295 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: DA 1296 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8540 (mm-30) REVERT: DL 74 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.4707 (mmt180) REVERT: DL 80 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7723 (mmm160) REVERT: DL 282 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.8038 (t60) REVERT: DB 276 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8754 (m) REVERT: DB 409 ASP cc_start: 0.9099 (m-30) cc_final: 0.8882 (m-30) REVERT: DB 607 MET cc_start: 0.9014 (mmt) cc_final: 0.8681 (mmt) REVERT: DB 874 GLU cc_start: 0.9414 (tp30) cc_final: 0.9211 (tp30) REVERT: DB 1168 ASP cc_start: 0.8665 (m-30) cc_final: 0.7855 (t0) REVERT: DC 92 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7766 (t80) REVERT: DC 498 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8374 (pp) REVERT: DE 185 GLU cc_start: 0.9070 (tt0) cc_final: 0.8810 (tt0) REVERT: DE 337 MET cc_start: 0.9113 (tpp) cc_final: 0.8801 (mmm) REVERT: DF 159 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8448 (t0) REVERT: DF 182 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7647 (mmt90) REVERT: DF 550 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9122 (m) REVERT: DG 15 ARG cc_start: 0.8984 (mtt-85) cc_final: 0.8780 (mtt-85) REVERT: DG 111 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7804 (mtt-85) REVERT: DG 226 GLU cc_start: 0.8998 (tp30) cc_final: 0.8670 (tp30) REVERT: DG 294 MET cc_start: 0.8991 (mtp) cc_final: 0.8767 (mtm) REVERT: DG 471 GLU cc_start: 0.8739 (tp30) cc_final: 0.8521 (pm20) REVERT: DH 141 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9080 (tp) REVERT: DH 377 ASP cc_start: 0.8917 (t70) cc_final: 0.8713 (t0) REVERT: DH 414 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9075 (mt) REVERT: DH 543 MET cc_start: 0.8619 (tpp) cc_final: 0.8265 (mmp) REVERT: DH 544 LYS cc_start: 0.8828 (tppt) cc_final: 0.8628 (ttpt) REVERT: DJ 186 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8745 (ttmt) REVERT: DK 135 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8594 (tpp-160) REVERT: DK 151 ASN cc_start: 0.9023 (m-40) cc_final: 0.8702 (m110) REVERT: DT 52 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8415 (ttm-80) REVERT: DT 126 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8622 (ttp-110) REVERT: DV 49 ASP cc_start: 0.9307 (t0) cc_final: 0.9104 (t0) REVERT: DV 56 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8496 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8566 (t0) cc_final: 0.8254 (t0) REVERT: DX 52 GLU cc_start: 0.8862 (pt0) cc_final: 0.8454 (pt0) REVERT: DX 103 MET cc_start: 0.8403 (mtp) cc_final: 0.8167 (mtp) REVERT: CC 10 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8626 (t) REVERT: CC 60 SER cc_start: 0.8839 (p) cc_final: 0.8595 (p) REVERT: CI 1 MET cc_start: 0.7112 (tmm) cc_final: 0.6703 (ttt) REVERT: CI 38 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9132 (mt) REVERT: CJ 37 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6000 (t0) REVERT: CJ 152 GLN cc_start: 0.8282 (tt0) cc_final: 0.7494 (mm110) REVERT: CJ 345 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8715 (m) REVERT: CJ 747 GLU cc_start: 0.8738 (pt0) cc_final: 0.8339 (tt0) REVERT: CJ 769 GLN cc_start: 0.8819 (tt0) cc_final: 0.8427 (mt0) REVERT: CN 31 MET cc_start: 0.9335 (mtt) cc_final: 0.8960 (mtm) REVERT: CN 32 TYR cc_start: 0.9200 (m-80) cc_final: 0.8808 (m-80) REVERT: CN 46 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8419 (mtp180) REVERT: CR 276 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7870 (mtt180) REVERT: CR 277 SER cc_start: 0.8795 (p) cc_final: 0.8587 (p) REVERT: CS 152 ASP cc_start: 0.8438 (p0) cc_final: 0.7947 (p0) REVERT: Cg 112 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8117 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.7993 (p-80) REVERT: Cg 238 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8429 (mmp-170) REVERT: Ci 82 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8272 (pm20) REVERT: Ci 89 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8445 (tpp) REVERT: Ci 105 ARG cc_start: 0.9194 (ptt-90) cc_final: 0.8976 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8024 (t70) REVERT: Ci 174 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8002 (t0) REVERT: Ck 38 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9039 (mm) REVERT: Ck 60 MET cc_start: 0.7536 (ptm) cc_final: 0.7174 (mtp) REVERT: Ck 166 MET cc_start: 0.8631 (mmt) cc_final: 0.8401 (mmm) REVERT: Ck 272 ASP cc_start: 0.8714 (m-30) cc_final: 0.8488 (m-30) REVERT: Ck 364 LEU cc_start: 0.7788 (mt) cc_final: 0.7490 (mp) REVERT: Ck 397 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7889 (mtm-85) REVERT: Ck 404 THR cc_start: 0.8812 (m) cc_final: 0.8472 (t) REVERT: Ck 414 MET cc_start: 0.8081 (ttm) cc_final: 0.7818 (tmm) REVERT: Ck 564 LEU cc_start: 0.8755 (mt) cc_final: 0.8467 (mt) REVERT: Ck 568 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6147 (pp) REVERT: Ck 843 MET cc_start: 0.5394 (ttt) cc_final: 0.5164 (ttp) outliers start: 199 outliers final: 145 residues processed: 1096 average time/residue: 0.7840 time to fit residues: 1427.5056 Evaluate side-chains 1054 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 884 time to evaluate : 6.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1244 LYS Chi-restraints excluded: chain DA residue 1295 GLN Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 272 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 282 TRP Chi-restraints excluded: chain DB residue 124 GLN Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 221 HIS Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 228 THR Chi-restraints excluded: chain DB residue 233 ASP Chi-restraints excluded: chain DB residue 276 VAL Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 464 THR Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 569 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 952 GLU Chi-restraints excluded: chain DC residue 1014 SER Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 405 ILE Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 58 ASP Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 182 ARG Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 162 LEU Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 220 THR Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 323 VAL Chi-restraints excluded: chain DG residue 341 ASN Chi-restraints excluded: chain DG residue 367 SER Chi-restraints excluded: chain DG residue 379 VAL Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 144 ASP Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 69 ASP Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 106 ASP Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 22 LYS Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 313 ASP Chi-restraints excluded: chain CI residue 351 MET Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 37 ASN Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 743 THR Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 777 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 76 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 218 THR Chi-restraints excluded: chain Cg residue 294 GLU Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ci residue 174 ASP Chi-restraints excluded: chain Ck residue 38 ILE Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 366 PHE Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 799 optimal weight: 0.8980 chunk 842 optimal weight: 5.9990 chunk 768 optimal weight: 6.9990 chunk 819 optimal weight: 2.9990 chunk 841 optimal weight: 7.9990 chunk 493 optimal weight: 0.9990 chunk 356 optimal weight: 0.3980 chunk 643 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 740 optimal weight: 5.9990 chunk 774 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 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 503 ASN ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DE 153 HIS ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DT 9 GLN DV 175 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 CI 55 GLN ** 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 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 738 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4376 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= 0.263 Angle : 0.516 10.284 107780 Z= 0.266 Chirality : 0.040 0.286 11595 Planarity : 0.005 0.096 13537 Dihedral : 11.383 177.156 12371 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.48 % Favored : 96.48 % Rotamer: Outliers : 2.62 % Allowed : 19.02 % Favored : 78.36 % 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: 1.17 (0.09), residues: 8966 helix: 1.70 (0.08), residues: 4252 sheet: 0.27 (0.26), residues: 393 loop : -0.05 (0.10), residues: 4321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCk 693 HIS 0.013 0.001 HISCg 296 PHE 0.019 0.002 PHEDC 123 TYR 0.018 0.001 TYRCJ 114 ARG 0.017 0.000 ARGDB 963 *********************** 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 1087 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 880 time to evaluate : 6.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1221 ILE cc_start: 0.9562 (mm) cc_final: 0.9355 (mt) REVERT: DA 1280 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8652 (mp0) REVERT: DL 74 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.4710 (mmt180) REVERT: DL 80 ARG cc_start: 0.8091 (mtp-110) cc_final: 0.7711 (mmm160) REVERT: DL 282 TRP cc_start: 0.8724 (OUTLIER) cc_final: 0.8397 (t60) REVERT: DL 305 THR cc_start: 0.8912 (m) cc_final: 0.8583 (p) REVERT: DB 276 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8769 (m) REVERT: DB 409 ASP cc_start: 0.9143 (m-30) cc_final: 0.8922 (m-30) REVERT: DB 508 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8609 (ptt180) REVERT: DB 607 MET cc_start: 0.9081 (mmt) cc_final: 0.8769 (mmt) REVERT: DB 942 ARG cc_start: 0.9306 (OUTLIER) cc_final: 0.9062 (ptp90) REVERT: DC 92 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.7696 (t80) REVERT: DC 498 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8432 (pp) REVERT: DE 634 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8957 (mtt90) REVERT: DF 159 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8116 (t0) REVERT: DF 550 VAL cc_start: 0.9384 (OUTLIER) cc_final: 0.9135 (m) REVERT: DG 111 ARG cc_start: 0.8015 (mmt180) cc_final: 0.7698 (mtt180) REVERT: DG 226 GLU cc_start: 0.9030 (tp30) cc_final: 0.8693 (tp30) REVERT: DG 294 MET cc_start: 0.9042 (mtp) cc_final: 0.8832 (mtm) REVERT: DH 141 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9110 (tp) REVERT: DH 377 ASP cc_start: 0.8997 (t70) cc_final: 0.8746 (t0) REVERT: DH 414 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9141 (mt) REVERT: DH 482 TYR cc_start: 0.8704 (m-80) cc_final: 0.8483 (m-80) REVERT: DH 484 ASP cc_start: 0.9097 (m-30) cc_final: 0.8884 (m-30) REVERT: DH 543 MET cc_start: 0.8659 (tpp) cc_final: 0.8303 (mmp) REVERT: DH 544 LYS cc_start: 0.8892 (tppt) cc_final: 0.8583 (tmtt) REVERT: DJ 186 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8759 (ttmt) REVERT: DK 151 ASN cc_start: 0.9030 (m-40) cc_final: 0.8654 (m110) REVERT: DT 52 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8444 (ttm-80) REVERT: DT 126 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8517 (ttp-110) REVERT: DV 56 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8491 (mtt-85) REVERT: DV 134 ASP cc_start: 0.8547 (t0) cc_final: 0.8259 (t0) REVERT: DX 103 MET cc_start: 0.8631 (mtp) cc_final: 0.8412 (mtp) REVERT: CC 10 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8746 (t) REVERT: CC 60 SER cc_start: 0.8865 (p) cc_final: 0.8630 (p) REVERT: CI 1 MET cc_start: 0.7247 (tmm) cc_final: 0.6722 (ttt) REVERT: CI 38 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9155 (mt) REVERT: CJ 37 ASN cc_start: 0.6689 (OUTLIER) cc_final: 0.5986 (t0) REVERT: CJ 50 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8829 (m-30) REVERT: CJ 130 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8524 (ptt90) REVERT: CJ 152 GLN cc_start: 0.8382 (tt0) cc_final: 0.7856 (mm110) REVERT: CJ 345 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8770 (m) REVERT: CJ 769 GLN cc_start: 0.8865 (tt0) cc_final: 0.8487 (mt0) REVERT: CN 31 MET cc_start: 0.9326 (mtt) cc_final: 0.8915 (mtm) REVERT: CN 32 TYR cc_start: 0.9252 (m-80) cc_final: 0.8850 (m-80) REVERT: CN 46 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8493 (mtp180) REVERT: CR 267 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8300 (p0) REVERT: CR 276 ARG cc_start: 0.8275 (tpp80) cc_final: 0.8026 (mtt180) REVERT: CR 277 SER cc_start: 0.8896 (p) cc_final: 0.8677 (p) REVERT: CS 152 ASP cc_start: 0.8546 (p0) cc_final: 0.8020 (p0) REVERT: Cg 112 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8123 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8031 (p-80) REVERT: Cg 238 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8475 (mmp-170) REVERT: Ci 89 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: Ci 105 ARG cc_start: 0.9186 (ptt-90) cc_final: 0.8958 (tmm-80) REVERT: Ci 136 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8085 (t70) REVERT: Ck 60 MET cc_start: 0.7593 (ptm) cc_final: 0.7210 (mtp) REVERT: Ck 166 MET cc_start: 0.8669 (mmt) cc_final: 0.8373 (mmm) REVERT: Ck 364 LEU cc_start: 0.7977 (mt) cc_final: 0.7694 (mp) REVERT: Ck 397 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7577 (mtm-85) REVERT: Ck 404 THR cc_start: 0.8757 (m) cc_final: 0.8541 (t) REVERT: Ck 414 MET cc_start: 0.8231 (ttm) cc_final: 0.7889 (tmm) REVERT: Ck 564 LEU cc_start: 0.8604 (mt) cc_final: 0.8332 (mt) REVERT: Ck 568 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6285 (pp) REVERT: Ck 843 MET cc_start: 0.5449 (ttt) cc_final: 0.5179 (ttp) outliers start: 207 outliers final: 154 residues processed: 1055 average time/residue: 0.7924 time to fit residues: 1388.8542 Evaluate side-chains 1043 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 863 time to evaluate : 6.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1244 LYS Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 282 TRP Chi-restraints excluded: chain DB residue 124 GLN Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 276 VAL Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 508 ARG Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 739 LEU Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 942 ARG Chi-restraints excluded: chain DB residue 949 THR Chi-restraints excluded: chain DB residue 950 VAL Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DB residue 1057 LEU Chi-restraints excluded: chain DB residue 1181 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 154 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 952 GLU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DE residue 46 SER Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 405 ILE Chi-restraints excluded: chain DE residue 634 ARG Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 58 ASP Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 80 VAL Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 202 LEU Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 544 SER Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 220 THR Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 323 VAL Chi-restraints excluded: chain DG residue 341 ASN Chi-restraints excluded: chain DG residue 362 SER Chi-restraints excluded: chain DG residue 367 SER Chi-restraints excluded: chain DG residue 379 VAL Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 144 ASP Chi-restraints excluded: chain DH residue 396 VAL Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 134 THR Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 69 ASP Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 103 LEU Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DW residue 108 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 22 LYS Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 49 ILE Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 313 ASP Chi-restraints excluded: chain CI residue 351 MET Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 37 ASN Chi-restraints excluded: chain CJ residue 50 ASP Chi-restraints excluded: chain CJ residue 130 ARG Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 743 THR Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 777 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CR residue 267 ASN Chi-restraints excluded: chain CR residue 274 VAL Chi-restraints excluded: chain CS residue 42 LEU Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 365 ASP Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ck residue 84 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 816 optimal weight: 0.0030 chunk 537 optimal weight: 0.9990 chunk 866 optimal weight: 8.9990 chunk 528 optimal weight: 8.9990 chunk 410 optimal weight: 4.9990 chunk 602 optimal weight: 0.8980 chunk 908 optimal weight: 6.9990 chunk 836 optimal weight: 0.9980 chunk 723 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 558 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1243 GLN DL 272 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 503 ASN ** DB 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DH 71 GLN ** 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 CI 55 GLN ** 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 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 34 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 79052 Z= 0.154 Angle : 0.478 11.150 107780 Z= 0.246 Chirality : 0.038 0.186 11595 Planarity : 0.004 0.093 13537 Dihedral : 11.290 178.239 12367 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.65 % Rotamer: Outliers : 2.34 % Allowed : 19.34 % Favored : 78.32 % 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: 1.26 (0.09), residues: 8966 helix: 1.78 (0.08), residues: 4249 sheet: 0.37 (0.26), residues: 386 loop : -0.00 (0.10), residues: 4331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPCk 693 HIS 0.009 0.001 HISCg 296 PHE 0.017 0.001 PHECJ 382 TYR 0.014 0.001 TYRDB 95 ARG 0.012 0.000 ARGDB 963 ********************** 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 1073 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 888 time to evaluate : 6.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: DA 1221 ILE cc_start: 0.9550 (mm) cc_final: 0.9342 (mt) REVERT: DA 1254 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6904 (mtm180) REVERT: DA 1280 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8661 (mp0) REVERT: DL 74 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.4697 (mmt180) REVERT: DL 80 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7718 (mmm160) REVERT: DL 282 TRP cc_start: 0.8576 (OUTLIER) cc_final: 0.8203 (t60) REVERT: DB 276 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8737 (m) REVERT: DB 409 ASP cc_start: 0.9086 (m-30) cc_final: 0.8859 (m-30) REVERT: DB 508 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8447 (ptt180) REVERT: DB 517 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8153 (mt-10) REVERT: DB 607 MET cc_start: 0.9055 (mmt) cc_final: 0.8736 (mmt) REVERT: DB 942 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.9021 (ptp90) REVERT: DB 967 ASP cc_start: 0.9502 (t0) cc_final: 0.8963 (t0) REVERT: DC 92 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.7714 (t80) REVERT: DC 498 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8448 (pp) REVERT: DE 337 MET cc_start: 0.9114 (tpp) cc_final: 0.8820 (mmm) REVERT: DE 634 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8915 (mtt90) REVERT: DF 159 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8304 (t0) REVERT: DF 544 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9018 (t) REVERT: DF 550 VAL cc_start: 0.9376 (OUTLIER) cc_final: 0.9148 (m) REVERT: DG 111 ARG cc_start: 0.8026 (mmt180) cc_final: 0.7707 (mtt180) REVERT: DG 226 GLU cc_start: 0.9026 (tp30) cc_final: 0.8684 (tp30) REVERT: DH 141 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9092 (tp) REVERT: DH 377 ASP cc_start: 0.8949 (t70) cc_final: 0.8737 (t0) REVERT: DH 414 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9127 (mt) REVERT: DH 484 ASP cc_start: 0.9121 (m-30) cc_final: 0.8872 (m-30) REVERT: DH 543 MET cc_start: 0.8607 (tpp) cc_final: 0.8255 (mmp) REVERT: DH 544 LYS cc_start: 0.8867 (tppt) cc_final: 0.8540 (ttpp) REVERT: DJ 186 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8732 (ttmt) REVERT: DK 99 ASP cc_start: 0.7773 (t0) cc_final: 0.7519 (t0) REVERT: DK 151 ASN cc_start: 0.9006 (m-40) cc_final: 0.8692 (m110) REVERT: DT 52 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8455 (ttm-80) REVERT: DT 126 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8612 (ttp-110) REVERT: DV 56 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8489 (mtt-85) REVERT: DX 103 MET cc_start: 0.8529 (mtp) cc_final: 0.8326 (mtp) REVERT: CC 10 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (t) REVERT: CI 1 MET cc_start: 0.7243 (tmm) cc_final: 0.6755 (ttt) REVERT: CI 38 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9136 (mt) REVERT: CJ 37 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6030 (t0) REVERT: CJ 50 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8779 (m-30) REVERT: CJ 152 GLN cc_start: 0.8392 (tt0) cc_final: 0.7741 (mm110) REVERT: CJ 769 GLN cc_start: 0.8794 (tt0) cc_final: 0.8405 (mt0) REVERT: CN 31 MET cc_start: 0.9327 (mtt) cc_final: 0.8945 (mtm) REVERT: CN 32 TYR cc_start: 0.9220 (m-80) cc_final: 0.8827 (m-80) REVERT: CN 46 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8417 (mtp180) REVERT: CR 276 ARG cc_start: 0.8334 (tpp80) cc_final: 0.8083 (mtt180) REVERT: CS 152 ASP cc_start: 0.8558 (p0) cc_final: 0.8042 (p0) REVERT: Cg 112 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8098 (mtm180) REVERT: Cg 127 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.7989 (p-80) REVERT: Cg 238 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8427 (mmp-170) REVERT: Ci 75 ASP cc_start: 0.9125 (p0) cc_final: 0.8878 (p0) REVERT: Ci 89 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8458 (tpp) REVERT: Ci 136 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8044 (t70) REVERT: Ck 60 MET cc_start: 0.7585 (ptm) cc_final: 0.7115 (mtp) REVERT: Ck 166 MET cc_start: 0.8658 (mmt) cc_final: 0.8429 (mmm) REVERT: Ck 364 LEU cc_start: 0.7944 (mt) cc_final: 0.7655 (mp) REVERT: Ck 397 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: Ck 404 THR cc_start: 0.8746 (m) cc_final: 0.8448 (t) REVERT: Ck 414 MET cc_start: 0.8218 (ttm) cc_final: 0.7893 (tmm) REVERT: Ck 564 LEU cc_start: 0.8678 (mt) cc_final: 0.8437 (mt) REVERT: Ck 568 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6301 (pp) outliers start: 185 outliers final: 148 residues processed: 1038 average time/residue: 0.8163 time to fit residues: 1410.7539 Evaluate side-chains 1046 residues out of total 7897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 874 time to evaluate : 6.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DA residue 1208 THR Chi-restraints excluded: chain DA residue 1244 LYS Chi-restraints excluded: chain DL residue 28 ASN Chi-restraints excluded: chain DL residue 41 ASP Chi-restraints excluded: chain DL residue 74 ARG Chi-restraints excluded: chain DL residue 267 HIS Chi-restraints excluded: chain DL residue 272 HIS Chi-restraints excluded: chain DL residue 274 THR Chi-restraints excluded: chain DL residue 282 TRP Chi-restraints excluded: chain DB residue 124 GLN Chi-restraints excluded: chain DB residue 146 MET Chi-restraints excluded: chain DB residue 227 THR Chi-restraints excluded: chain DB residue 276 VAL Chi-restraints excluded: chain DB residue 329 VAL Chi-restraints excluded: chain DB residue 424 ASP Chi-restraints excluded: chain DB residue 439 VAL Chi-restraints excluded: chain DB residue 508 ARG Chi-restraints excluded: chain DB residue 521 LEU Chi-restraints excluded: chain DB residue 624 VAL Chi-restraints excluded: chain DB residue 733 HIS Chi-restraints excluded: chain DB residue 743 VAL Chi-restraints excluded: chain DB residue 756 THR Chi-restraints excluded: chain DB residue 810 THR Chi-restraints excluded: chain DB residue 878 VAL Chi-restraints excluded: chain DB residue 901 VAL Chi-restraints excluded: chain DB residue 908 GLN Chi-restraints excluded: chain DB residue 920 VAL Chi-restraints excluded: chain DB residue 942 ARG Chi-restraints excluded: chain DB residue 950 VAL Chi-restraints excluded: chain DB residue 1009 ASP Chi-restraints excluded: chain DB residue 1057 LEU Chi-restraints excluded: chain DC residue 30 THR Chi-restraints excluded: chain DC residue 92 PHE Chi-restraints excluded: chain DC residue 119 THR Chi-restraints excluded: chain DC residue 162 ILE Chi-restraints excluded: chain DC residue 240 VAL Chi-restraints excluded: chain DC residue 268 ASP Chi-restraints excluded: chain DC residue 350 ASP Chi-restraints excluded: chain DC residue 495 THR Chi-restraints excluded: chain DC residue 498 LEU Chi-restraints excluded: chain DC residue 766 VAL Chi-restraints excluded: chain DC residue 839 VAL Chi-restraints excluded: chain DC residue 873 VAL Chi-restraints excluded: chain DC residue 874 THR Chi-restraints excluded: chain DC residue 894 HIS Chi-restraints excluded: chain DC residue 952 GLU Chi-restraints excluded: chain DC residue 1071 VAL Chi-restraints excluded: chain DC residue 1076 PHE Chi-restraints excluded: chain DC residue 1122 THR Chi-restraints excluded: chain DC residue 1153 LEU Chi-restraints excluded: chain DE residue 212 LEU Chi-restraints excluded: chain DE residue 299 LYS Chi-restraints excluded: chain DE residue 398 LEU Chi-restraints excluded: chain DE residue 405 ILE Chi-restraints excluded: chain DE residue 634 ARG Chi-restraints excluded: chain DF residue 13 ILE Chi-restraints excluded: chain DF residue 58 ASP Chi-restraints excluded: chain DF residue 69 THR Chi-restraints excluded: chain DF residue 72 THR Chi-restraints excluded: chain DF residue 80 VAL Chi-restraints excluded: chain DF residue 146 GLU Chi-restraints excluded: chain DF residue 157 THR Chi-restraints excluded: chain DF residue 159 ASP Chi-restraints excluded: chain DF residue 227 THR Chi-restraints excluded: chain DF residue 258 ASP Chi-restraints excluded: chain DF residue 544 SER Chi-restraints excluded: chain DF residue 550 VAL Chi-restraints excluded: chain DG residue 30 SER Chi-restraints excluded: chain DG residue 36 THR Chi-restraints excluded: chain DG residue 91 LYS Chi-restraints excluded: chain DG residue 210 VAL Chi-restraints excluded: chain DG residue 220 THR Chi-restraints excluded: chain DG residue 238 ASN Chi-restraints excluded: chain DG residue 273 VAL Chi-restraints excluded: chain DG residue 300 ASP Chi-restraints excluded: chain DG residue 323 VAL Chi-restraints excluded: chain DG residue 341 ASN Chi-restraints excluded: chain DG residue 362 SER Chi-restraints excluded: chain DG residue 367 SER Chi-restraints excluded: chain DG residue 379 VAL Chi-restraints excluded: chain DG residue 384 VAL Chi-restraints excluded: chain DH residue 40 THR Chi-restraints excluded: chain DH residue 79 ASP Chi-restraints excluded: chain DH residue 80 ARG Chi-restraints excluded: chain DH residue 141 LEU Chi-restraints excluded: chain DH residue 144 ASP Chi-restraints excluded: chain DH residue 318 GLU Chi-restraints excluded: chain DH residue 414 LEU Chi-restraints excluded: chain DH residue 436 VAL Chi-restraints excluded: chain DH residue 460 LEU Chi-restraints excluded: chain DH residue 476 VAL Chi-restraints excluded: chain DJ residue 55 ASN Chi-restraints excluded: chain DJ residue 100 VAL Chi-restraints excluded: chain DJ residue 149 THR Chi-restraints excluded: chain DJ residue 166 LEU Chi-restraints excluded: chain DJ residue 186 LYS Chi-restraints excluded: chain DJ residue 226 VAL Chi-restraints excluded: chain DJ residue 323 THR Chi-restraints excluded: chain DK residue 22 SER Chi-restraints excluded: chain DK residue 34 ASN Chi-restraints excluded: chain DK residue 265 VAL Chi-restraints excluded: chain DT residue 65 VAL Chi-restraints excluded: chain DT residue 90 THR Chi-restraints excluded: chain DT residue 140 ASN Chi-restraints excluded: chain DT residue 205 VAL Chi-restraints excluded: chain DV residue 25 SER Chi-restraints excluded: chain DV residue 43 ASN Chi-restraints excluded: chain DV residue 56 ARG Chi-restraints excluded: chain DV residue 114 VAL Chi-restraints excluded: chain DV residue 127 THR Chi-restraints excluded: chain DV residue 143 ILE Chi-restraints excluded: chain DW residue 60 VAL Chi-restraints excluded: chain DX residue 76 ARG Chi-restraints excluded: chain DX residue 132 THR Chi-restraints excluded: chain DX residue 150 SER Chi-restraints excluded: chain DX residue 162 VAL Chi-restraints excluded: chain DY residue 19 THR Chi-restraints excluded: chain DY residue 50 VAL Chi-restraints excluded: chain DY residue 132 ASP Chi-restraints excluded: chain CC residue 10 VAL Chi-restraints excluded: chain CC residue 15 ILE Chi-restraints excluded: chain CC residue 22 LYS Chi-restraints excluded: chain CC residue 24 LYS Chi-restraints excluded: chain CC residue 49 ILE Chi-restraints excluded: chain CC residue 69 GLU Chi-restraints excluded: chain CI residue 38 LEU Chi-restraints excluded: chain CI residue 313 ASP Chi-restraints excluded: chain CI residue 351 MET Chi-restraints excluded: chain CI residue 415 LEU Chi-restraints excluded: chain CI residue 423 GLU Chi-restraints excluded: chain CI residue 435 LYS Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CJ residue 37 ASN Chi-restraints excluded: chain CJ residue 50 ASP Chi-restraints excluded: chain CJ residue 178 SER Chi-restraints excluded: chain CJ residue 235 GLU Chi-restraints excluded: chain CJ residue 332 GLU Chi-restraints excluded: chain CJ residue 345 VAL Chi-restraints excluded: chain CJ residue 403 CYS Chi-restraints excluded: chain CJ residue 409 SER Chi-restraints excluded: chain CJ residue 490 ASP Chi-restraints excluded: chain CJ residue 550 GLU Chi-restraints excluded: chain CJ residue 552 ILE Chi-restraints excluded: chain CJ residue 743 THR Chi-restraints excluded: chain CJ residue 770 THR Chi-restraints excluded: chain CJ residue 777 THR Chi-restraints excluded: chain CJ residue 803 ILE Chi-restraints excluded: chain CN residue 111 VAL Chi-restraints excluded: chain CS residue 61 THR Chi-restraints excluded: chain CS residue 105 VAL Chi-restraints excluded: chain CS residue 119 VAL Chi-restraints excluded: chain Cg residue 30 VAL Chi-restraints excluded: chain Cg residue 42 THR Chi-restraints excluded: chain Cg residue 112 ARG Chi-restraints excluded: chain Cg residue 127 HIS Chi-restraints excluded: chain Cg residue 173 THR Chi-restraints excluded: chain Cg residue 251 HIS Chi-restraints excluded: chain Cg residue 296 HIS Chi-restraints excluded: chain Cg residue 383 ASP Chi-restraints excluded: chain Ci residue 82 GLN Chi-restraints excluded: chain Ci residue 89 MET Chi-restraints excluded: chain Ci residue 136 HIS Chi-restraints excluded: chain Ck residue 61 LEU Chi-restraints excluded: chain Ck residue 84 THR Chi-restraints excluded: chain Ck residue 137 THR Chi-restraints excluded: chain Ck residue 159 THR Chi-restraints excluded: chain Ck residue 318 THR Chi-restraints excluded: chain Ck residue 410 LEU Chi-restraints excluded: chain Ck residue 568 LEU Chi-restraints excluded: chain Ck residue 585 MET Chi-restraints excluded: chain Ck residue 606 THR Chi-restraints excluded: chain Ck residue 810 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 912 random chunks: chunk 443 optimal weight: 2.9990 chunk 574 optimal weight: 0.0670 chunk 770 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 667 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 724 optimal weight: 1.9990 chunk 303 optimal weight: 0.1980 chunk 744 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA1243 GLN DL 272 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 503 ASN ** DB 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DE 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DF 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** DK 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DW 23 HIS DW 72 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 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 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cg 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 34 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.094808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.076071 restraints weight = 141308.050| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.67 r_work: 0.2745 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 79052 Z= 0.146 Angle : 0.477 11.066 107780 Z= 0.244 Chirality : 0.037 0.181 11595 Planarity : 0.004 0.116 13537 Dihedral : 11.244 178.338 12364 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 2.28 % Allowed : 19.40 % Favored : 78.32 % 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: 1.30 (0.09), residues: 8966 helix: 1.81 (0.08), residues: 4243 sheet: 0.39 (0.26), residues: 388 loop : 0.02 (0.10), residues: 4335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPCk 693 HIS 0.017 0.001 HISDL 272 PHE 0.017 0.001 PHECJ 382 TYR 0.021 0.001 TYRCC 70 ARG 0.012 0.000 ARGDB 963 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24664.38 seconds wall clock time: 430 minutes 42.41 seconds (25842.41 seconds total)